In a culture that promotes alternative medicine, natural childbirth, and sometimes-bizarre dietary supplements, it seems strange that natural infertility treatments are not well-known. A natural infertility treatment is not necessarily alternative medicine, but rather a conventional-medicine approach that seeks to cure the underlying cause of infertility, allowing natural conception. It stands in contrast to assisted reproductive technology such as in vitro fertilization (IVF), which is stick a "band-aid" solution that does nothing about the underlying causes of fertility problems.

Why is assisted reproductive technology the current standard of care for infertility? If you type "fertility treatment" into Wikipedia, you are redirected to "assisted reproductive technology." Wikipedia, being written collaboratively by people around the world, reflects the biases and attitudes of those people. Fertility drugs and IVF are what people think of when they think about infertility treatments.

I think the reason IVF is so popular — despite its astronomical cost and mediocre success rate (only 1 in 3 attempts results in a live birth) — is because it is a "magic pill" approach. It is a silver bullet, a straightforward process left in the hands of doctors. Natural fertility treatments are more complicated because they start with diagnostics, rather than jumping immediately into treatment.

Among the diagnostic steps used in natural fertility treatments for women are ultrasound, laparoscopy, and sonohysterosalpingography (SHSG) to look for structural problems in the reproductive organs, as well as hormone level checks. During her menstrual cycle, a woman's estrogen and progesterone levels can change significantly in as little as 24 hours, so daily or every-other-day tests are best. Any underlying disease or structural abnormality that is uncovered is treated to increase the odds of a naturally conceived pregnancy.

How successful is natural infertility treatment compared to assisted reproductive technology? IVF has a maximum success (pregnancy) rate well under 50% (for 27-year-old women), with an average success rate closer to 35%. Statistics for live birth are even worse, with an average of only about 27% of attempts resulting in live births. That means that an average of 8% of attempts result in a miscarriage or stillbirth (or, if the fetus is imperfect, abortion). The poor success rates reflect, in part, the fact that over 50% of embryos conceived in vitro have chromosomal abnormalities, as reported by Rebecca Taylor of Mary Meets Dolly. Natural fertility technology also has treatments for male infertility.

According to the Pope Paul VI institute, a major proponent of natural infertility treatment, so-called "natural reproductive technology" has higher success rates than IVF for various infertility diagnoses. These results are both statistically significant (i.e. not due to chance) and personally significant (i.e. they're a lot higher). For example, for a diagnosis of endometriosis, IVF has a success (pregnancy) rate of about 21%, while natural reproductive treatment has a success rate of about 57%. It reports a 37% success rate for tubal occlusion compared to IVF's 27%. The whopping 82% success rate reported for natural fertility treatment of anovulation (not producing mature eggs) may be due to straightforward treatment of the most obvious cause of anovulation, hormonal insufficiency (although I am speculating here).

I find it amazing that natural treatments for infertility are not better-known, even though they are more effective than current approaches. That's right: for infertile couples, it is more effective to try to conceive a baby the way nature always has than to inject a sperm into an egg under a microscope, with less chance of complications like chromosomal abnormalities and multiple gestation. Who wouldn't choose that first, if they knew it was available?

Image credit: "Test tube baby" by Brendan Dolan-Gavitt. (CC) Some rights reserved.

Scientific American published a tongue-in-cheek piece advocating a reclassification of dog breeds into different species of dog. The author has a point: If a species is defined as a reproductively isolated population, then surely some breeds are reproductively isolated from others (the mastiff and the Chihuahua are mentioned).

Following this line of reasoning, dogs would be most accurately described as a "ring species," in which there is a continuum of gradually varying — and potentially interbreeding — forms with two "ends" incapable of interbreeding. The mastiff and the Chihuahua are at the ends. But a German shepherd and a Labrador retriever, on the other hand, could certainly populate the animal shelters with hybridized mutts. And surely that Chihuahua could have some success, so to speak, with a Yorkshire terrier.

Some dog breeds are not capable of reproducing at all, at least not without technological intervention. French bulldog females usually must be artificially inseminated because males cannot mount effectively, and the puppies often must be delivered by Caesarian section. I am not sure how such creatures would fit into the classical species definition. It was not designed for populations that can't reproduce at all!

The impetus behind the proposed dog reclassification was to demonstrate that, in fact, speciation has been observed. Biblical literalist creationists often claim that science has never observed the splitting of one species into two different species.

Alas, if you know Creationists, you know this would not work. First, speciation has been observed already, and Creationists have no problem denying it. (See the Talk Origins information on observed speciation, an Internet classic.) Second, when a Creationist talks of a "species," he does not mean a reproductively isolated population. He means a "kind," sometimes called a "baramin," a concept exclusive to literal Creationism (i.e. not found in science). The Creationist would argue that the various canine breeds, along with wolves and wild dogs, comprise the dog "kind," and that while there might be "microevolution" within the kind, no dog would ever evolve into a new"kind." (Presumably, divine intervention would prevent "microevolution" from going too far.)

The proposal to call dog breeds different species was not made seriously. But it's good to think about the species concept once in a while.

Image credit: Ellen Levy Finch, licensed under the GFDL.

My stem cell articles for Bright Hub for March have been published. There are some articles about treatments. If you only read one, read the one about induced pluripotent stem cells (iPSCs). These show incredible promise as a controvery-free replacement for embryonic stem cells.

• Induced Pluripotent Stem Cells (iPS cells)
• Problems With Embryonic Stem Cell Treatments
• Stem Cell Treatments for Paralysis (both embryonic stem cells and adult stem cells)
• The Cutting Edge of Stem Cell Research — amazing advances with adult stem cells

Stem cell research is moving so fast that it is hard to keep up. Already there are clinical trials that may actually heal spinal cord injuries. Unfortunately, they use embryonic stem cells. Amazingly, embryonic stem cells may not even be necessary for this treatment; adult stem cells have healed spinal cord injuries in rats, just like embryonic stem cells.

I recently read the book Traffic: Why We Drive the Way We Do (and What It Says About Us) by Tom Vanderbilt, a fascinating look at many aspects of car culture: how roads affect traffic patterns, how both safety and danger are often an illusions, how driving behavior varies around the world, and how traffic deaths are correlated not to GDP or highway spending, but to governmental corruption. This book examines a lot of psychological science and the intersection (hah) between psychology and engineering that goes into traffic management.

It turns out that traffic engineering is not rocket science. It's way more complicated than that.

For example, road capacity is directly related to the demand for road capacity. In other words, if traffic engineers put in a new lane or road to ease congestion on an existing road, they will be confounded by a number of new drivers on that road. Adding to capacity somehow adds to the number of drivers using it (and vice versa: when roads or lanes are removed, for instance by construction, demand falls). This peculiar phenomenon stems from the fact that drivers are independent beings who make choices based on what is available to them. If a road is too crowded, some will choose to make fewer trips (perhaps telecommuting or combining errands into one trip). If new capacity becomes available, some will choose to make more trips (perhaps not making the effort of combining errands into a single trip).

I have some questions for you, dear reader, and would love it if you shared your thoughts in the comments below.

1. What are your traffic pet peeves? What driver behaviors and road conditions drive (hah) you crazy?
2. Do you think you are an average driver, in terms of skill and safety? Below or above average? Why?
3. What do you think of the use of the horn? Is it always rude? When is it not rude?
4. And where do you do most of your driving? I'm wondering about geography, since traffic culture varies widely among locations. New York drivers are very different from London drivers or Salt Lake City drivers.
   

The Scientific American headline asks, "Can Babies Be Made to Order?" It is typical of SciAm, as well as of many members of the research community, that the more important question was overlooked: "Should Babies Be Made to Order?"

The article is an interview with Maria Lalioti, an expert in pre-implantation genetic diagnosis, or PGD. In PGD, embryos are created in vitro and then screened for certain genetic traits, which may include traits incompatible with life or merely traits that increase risk for certain diseases.

The embryos that fail the screening are labelled "undesirable." I'm not making that up: Lalioti says the parents decide the fate of "undesirable embryos" whose genes are imperfect. They may be experimented on, or they may be killed. Lalioti's euphemisms, respectively, are "donated to science" and "discarded."

Let us be crystal clear about what PGD does and does not do. PGD does not save lives — it takes them. It kills young, tiny humans before a couple invests significant affection and financial resources on them. It kills them before they are cute enough to inspire sympathy.

PGD is a ghastly "solution" to preventing diseases with a genetic component. It's the solution of Adolf Hitler, who also took undesirable people and discarded them or donated them to science. At least his victims could look their killers in the eye.

The real kicker occurs near the end of the interview, in which Lalioti self-righteously announces that her clinic does not permit sex selection of interviews "for ethical reasons." She derisively adds that some clinics "are making a lot of money" doing just this.

As for the question "Can Babies Be Made to Order?" The answer, according to Lalioti, is probably not. We don't know enough about the genes that influence cosmetic traits like hair and eye color. After all, researching those genes does nothing to teach us how to save lives. PGD does not save lives, either; it takes them.

Correction: When first published, this post incorrectly stated that Dr. Lalioti's clinic "does permit sex selection." This was a typo; it was supposed to read "does not permit sex selection." The error has been corrected and I apologize for any misunderstanding.

You may know that I write science articles for the a science and technology website called Bright Hub. I just completed a short series on the basics of stem cells: terminology, classification, and sources. Each article is meant to stand alone, so they are a little repetitive.

These are not opinion pieces, so I did not express my personal strenuous opposition to any use of embryonic stem cells. I did carefully note in every article in which embryonic stem cells are mentioned that harvesting embryonic stem cells kills the embryo.

Only one article is about stem cell treatments. That's because I was only assigned to write one. Here are the links:

• Facts about stem cells
• Types of stem cells
• How stem cells are harvested
• Cloning and stem cells
• Heart disease treatment with stem cells

Would you like to see me write more about stem cells? Are there any particular topics you would like to see covered? I can always write as much as I like in this space, and I can ask my editor for more stem cell assignments at Bright Hub.

I am jumping on a meme bandwagon: Seven Quick Takes Friday, hosted by Jen F. at Conversion Diary. Since this is a blog about science and faith, not a personal diary, I hope Jen will forgive me if my seven snippets consist of news, info, and thoughts about those subjects.

1.

If you grow your young in a uterus, but you have not evolved a placenta, how do you feed them? For the gray nurse shark, aka the sand tiger shark, the answer is incestuous cannibalism. Gray nurse shark pups in the womb eat each other for nourishment, so only two are born per pregnancy (females have two uteruses). Since they are endangered, marine biologist Nick Otway is trying to develop an artificial uterus for gray nurse shark pups. Back when I worked as an aquarium biologist, we had several of these huge sharks. They are quite docile despite their fearsome complement of teeth.

At right: Grey nurse shark at the Minnesota Zoo, courtesy Joe Lencioni. (CC) Some rights reserved.

2.

Check out this video of comedian Stephen Crowder, hosted by the Raving Theist (formerly the Raving Atheist). He does an over-the-top parody comparing Planned Parenthood to a used car salesman.

3.

From the world of physics (via Scientific American) comes a story about the continued dissonance between Einstein's special relativity and quantum mechanics. This particular story has to do with a principle of special relativity called locality, which conflicts with a principle of quantum mechanics called entanglement. Of note is a comment buried on page 4 of the online article:

The old aspirations of physics to be a guide to metaphysics, to tell us literally and straightforwardly how the world actually is—aspirations that had lain dormant and neglected for more than 50 years—began, slowly, to reawaken.

This is good news for philosophers who, like me*, view reality as a concrete thing and truth as absolute.

*Not that I am any kind of philosopher.

4.

Shame on the New York Times for its headline, "For Catholics, a Door to Absolution is Reopened." The article is about the church's promotion of indulgences — which are decidedly not the same as absolution, and which have never had the door closed, having always been available. The Times notes that the tradition of indulgences is "one of the most complicated to explain," then proceeds to do a rotten job of explaining it. In particular is the omission of the crucial point that Purgatory is a process of purification, of making us more like God so we can enter his heaven, not a place in space-time where one serves a sentence of days or years. (Hat tip to Science and Religion News.)

5.

When Pluto was removed from the list of planets, it became the first discovered member in a brand-new class of space objects: the dwarf planets. In a way, this is actually a promotion, not a demotion. But apparently a lot of people are emotionally attached to Pluto as a planet. In 2007, the State of New Mexico (home of Pluto's discoverer, Clyde Tombaugh) declared Pluto officially a planet. (Hat tip to Spaceports blog.) This reminds me of the apocryphal tale of one of the Appalachian states (Tennessee?) trying to declare the mathematical constant pi as equal to exactly 3.

At right: Image of Pluto and its moons by the Hubble Space Telescope (courtesy of NASA).

6.

If you are Catholic, and the Pope himself told you to your face that you were wrong on some issue, would you reconsider your position? Apparently, Nancy Pelosi would not. She shows no signs of easing from her pro-choice stance despite a face-to-face reprimand from Pope Benedict XVI. One prays that at least a seed was planted.

7.

Until now, the Alavesia fly was an insect known only from amber fossils from the Cretaceous period, before the mass extinction that killed the dinosaurs and many other species. Now two species of living Alavesia have been found in Namibia and have been dubbed "living fossils" by the media. A completely new suborder of insects, the Mantophasmatodea, was discovered as well. There is still much we do not know about the mysterious world of living things. It's no surprise the new discoveries were insects; there are an estimated six to ten million species of insects, but only about a million have been described.

This post is a contribution to the blog swarm "Blog for Darwin," held from February 12-15, 2009, to celebrate the 200th anniversary of Charles Darwin's birth.

When Charles Darwin published On the Origin of Species in 1859, introducing the world to the revolutionary concept of evolution through natural selection, he noted that "perhaps ... the most obvious and gravest objection which can be urged against my theory" was the apparent lack of "transitional" fossils in the geological record. He speculated that the reason that "geology ... does not reveal [a] finely graded organic chain" of intermediate forms was because of the paucity of fossil discoveries at the time.

In one sense, every species that has ever existed is a "transitional" form; it reflects characteristics of its ancestors, and its characteristics will be reflected in its descendants. But humans are impressed by the dramatic, and in the years since Darwin's first book on evolution was published, some very dramatic fossils, intermediate between two large classes, have been discovered.

The most famous of these is Archaeopterix, which depending on one's interpretation is either a a bird with teeth and clawed hands or a feathered, flying dinosaur. But another lesser-known fossil is equally dramatic as an example of a transitional form: the marvelous Ichthyostega.

Ichthyostega is an intermediate form between fishes and amphibians from the late Devonian period, about 365 million years ago. One could describe it as a fish with legs that could walk around on land, or one could say it was an amphibian with the head and tail of a fish. Since fish have their weight supported by the water, Ichthyostega faced the problem of supporting its weight on land, which was accomplished by thickened, overlapping ribs — a clumsy, primitive solution necessary because it had so recently evolved from its lungfish-like ancestors.

Ichthyostega had seven toes on each hind foot, notable since the number of toes on tetrapod* feet stabilized at five early in their evolution. Its shoulder and hip had adaptations to help it move about on land. Its hind limbs could support its body as a juvenile, but were likely too weak to support its full weight on land in adulthood. It is hypothesized that juveniles could leave the water to escape predators, but adults only partially pulled themselves out of the water to sun themselves.

Ichthyostega is one of many fossils that fill in the natural history of the evolution of tetrapods from fish. The story is still not complete: "Romer's gap" (named after paleontologist Alfred Sherwood Romer) is a 20 million year period of missing fossils between Ichthyostega and its contemporaries and the next-oldest known tetrapods.

Gaps in the fossil record like this were a worry to Darwin, who recognized them as a potential rebuttal of his seminal theory. Yet absence of evidence is not evidence of absence; the most parsimonious explanation for Romer's gap remains the one Darwin put forth — the incompleteness of the geological record. Charles Darwin's extraordinary theory is now secure as one of the most well-established, concrete principles of biology.

*Tetrapods are four-legged vertebrates and their descendants; in other words, all vertebrates except fish.

More information on Ichthyostega

• Ichthyostega from the Tree of Life web project
• Cladogram showing Ichthyostega's place in the evolution of tetrapods (Palaeos database)

Ichthyostega image information

• Top right: Reconstruction of a juvenile Ichthyostega from the National Museum of Natural Science in Taiwan. Photo by Alton Thompson. (CC) Some rights reserved.
• Left: Pencil drawing of Ichthyostega. From Wikimedia Commons, licensed under the GNU Free Documentation License (GFDL).
• Bottom right: Drawing of Ichthyostega skeleton. The forelimbs are incompletely fossilized and the hand morphology is unknown. From the Tree of Life web project (link above), after Ahlberg et al. 2005. (CC) Some rights reserved.
  

The youngest Leave the lights on blogger, my 14-month-old son, got three shots last week. He and his brother have had every vaccination recommended by pediatricians. I understand that a lot of parents are hesitant about vaccinations because of fears of their safety. Those parents should fear for the safety of their children if they don't vaccinate.

Vaccines are safe

Most of the fears about vaccinations center on the purported link between the mercury-based preservative thimerosal and autism. But study after study — most recently, one conducted in Italy — have shown that thimerosal does not cause autism. In fact, the original study that suggested the thimerosal-autism link was faked. And even if this evidence is not convincing, thimerosal is no longer used in most vaccinations.

Not vaccinating can be deadly

Last month in Minnesota, a seven-month-old baby died of Hib, or Haemophilus influenzae type b. Hib infections are vanishingly rare in the U.S. because of the routine use of the Hib vaccine, which is given at 2, 4, 6, and 12 months (this is one of the shots my son received last month). The child who died, and two of four other kids who were sickened by the Hib outbreak, were unvaccinated "because of their parents' decisions." In other words, the parents decided not to protect their children against deadly infections.

Of the other two children, one was only five months old and so had not completed the primary 3-shot series. The other had an immune deficiency. When vaccination rates are above a certain "threshold," people like these two children are protected by "herd immunity" (a term that originated in animal husbandry). The disease cannot spread because there are not enough vulnerable individuals in the population. When people choose not to be vaccinated, or not to have their children vaccinated, herd immunity suffers, and people like these two babies can be sickened.

The refusal to vaccinate one's children is a source of frustration for health officials. I cannot understand a parent's reluctance to protect their children against deadly diseases that should only be a memory in the twenty-first century.

It's almost the weekend, so let's talk about TV.

I watch FOX's House regularly. I am losing interest in the program because (besides becoming clichéd and boring) it is not realistic.

The medical cases themselves are full of inaccuracies; one is tempted to uncharitably call them lies. One character is "dying" of Huntington's chorea, which in reality is not a fatal disease at all. A patient died of acute eclampsia a month after giving birth — never mind that eclampsia is cured by delivery of the baby. In one especially infamous episode, a psychiatric condition called "mirror syndrome" was completely invented out of thin air by the writers. (There is a real condition called mirror syndrome which affects pregnant women; this illness was also featured in an episode. Oops.)

Each episode begins with an apparently healthy patient dramatically (and often graphically) collapsing. They are then whisked to Dr. House's hospital, where his team of crack doctors (a bunch who apparently failed medical ethics in school) personally conduct the procedures and tests that are normally done by nurses, radiologists, and other specialists. Dr. House invariably treats the patient more callously than can be imagined, often being deliberately cruel — and clearly delighting in it. At the end, Dr. House (or, less freqeuntly, another doctor, such as the skankily-dressed hospital administrator Dr. Cuddy) has a brilliant flash of insight that tells him the patient's true diagnosis, and treatment after that is quick and easy (unless it is incurable and the patient dies, which happens fairly often).

Scientific American blogger Jordan Lite notes that the cases are often taken from the New England Journal of Medicine's clinical problem-solving column, and that one writer-producer, David Foster, is an M.D. A book has even been written about the show, The Medical Science of House, M.D. But I find the science unrealistic. This is not how medicine is works.

A real mystery disease is usually chronic. A patient with a real "zebra" condition has usually seen many doctors. Once a diagnosis is made, if it is made, treatment is not necessarily quick and easy.

Also, a good doctor is not cruel.

CNN recently featured a story on Dr. William Gahl, who is a real-life diagnostician of rare diseases. Read this story for a realistic picture of how doctors approach medical mysteries. And keep watching House, if you enjoy it. But remember that it's just as fictional with its science as Star Trek and Battlestar Galactica.

As a follow-up to my post listing definitions related to the beginning of human life, here are some diagrams I drew (using my mad skills in Microsoft Paint) illustrating how human fertilization takes place. These raster drawings do not do justice to the miracle of the beginning of a human life, but I hope they clarify the technical aspects.

	The egg and sperm immediately before fertilization. Each has a haploid nucleus containing one of every chromosome.*
	The cell membranes of the egg and sperm fuse. This can be said to be the moment of fertilization. Instead of two gametes, there is now a single zygote.
	As the cell membrane fusion is completed, the nuclei remain separate. The cell itself is thus diploid (containing two copies of every chromosome), but instead of one diploid nucleus, it contains two haploid nuclei. The sperm's tail degenerates.
	The nuclear membranes (not shown) dissolve and the chromosomes replicate. The result is that the zygote now contains two diploid sets of DNA in preparation for the first cell division (mitosis).
	The DNA intermingles into two bodies of chromosomes, each of which comes half from the egg and half from the sperm. These begin to undergo mitosis.
	A cell membrane forms across the middle of the zygote, resulting in two cells. It is now an embryo, not a zygote. Each cell contains a diploid nucleus containing a full copy of both the egg's and the sperm's chromosomes.

*For the sake of simplicity, I omitted the completion of meiosis in the egg's nucleus from these illustrations.

If you read any of the many blogs or news sources that deals with bioethics, then you will have heard of the story from the BBC that a British fertility doctor has successfully performed eugenics via in vitro fertilization. He tested embryos for a gene that is associated with an increased risk of breast cancer, and implanted only those embryos that were pure enough to meet his standards; the rest were killed (euphemistically, "discarded"). What was really remarkable about the story was the ridiculous attempt to redefine standard medical terminology to make the act more palatable. Conception is synonymous with fertilization, but the BBC parroted the doctor in incorrectly claiming that conception is actually synonymous with implantation. This allows the doctors to pretend that the genetic test took place before any human individuals were created by saying it was "pre-conception." For more information, see this post on the blog Mary Meets Dolly.

For the benefit of readers who may encounter mendacious doctors and scientists who deal with beginning-of-life issues, here is a glossary of related terms:

abortifacient

A drug or other substance that induces an abortion. Abortifacients may cause expulsion of the embryo or fetus, killing it, or they may prevent the implantation of an embryo. In the narrowest clinical sense, the latter is not technically the termination of a pregnancy, but it does result in the killing of the embryo.

abortion

The termination of a pregnancy; usually used for terminations before about 20 weeks gestation. Abortions may be spontaneous and natural (in which case they are also called miscarriages) or intentional (in which case they are also called induced abortions). An abortion always results in the death of the embryo or fetus.

adult stem cell

Any stem cell derived from an individual after the embryonic stage of development. Despite the name, they can be obtained from fetuses, umbilical cords, and children as well as from adults. Adult stem cells vary widely in potency. They can be obtained without injuring the donor.

baby

A non-scientific, non-specific term referring to a young human individual. Depending on context, it can refer to a zygote, embryo, fetus, newborn, or older child. Obstetricians routinely refer to embryos and fetuses as "babies" when the pregnancy is wanted, but not if the mother intends to abort the pregnancy. See abortion.

chromosome

A unit of genetic material. Every species has a fixed number of chromosomes.

conception

Synonymous with fertilization.

diploid

Having two copies of each chromosome per cell. In mammals, all cells except gametes are diploid.

egg

Also called an ovum, a female gamete. In humans, eggs are very large cells that are usually produced one at a time.

embryo

An organism from the time of the first cell division to a set point such as birth or hatching. In humans, an individual from the first cell division after conception until eight weeks after conception (ten weeks gestation), at which point it is called a fetus.

embryonic stem cell

A stem cell taken from an embryo. Embryonic stem cells are pluripotent, meaning they can differentiate into almost any tissue type. They are obtained by removing the embryo's inner cell mass, killing the embryo.

eugenics

The practice of attempting to improve the human race by either killing individuals perceived as genetically inferior, preventing such individuals from reproducing, or encouraging increased reproduction for individuals perceived as superior.

fertilization

The union of a haploid egg and a haploid sperm, resulting in a new, independent diploid individual. Fertilization naturally takes place in a woman's Fallopian tube after sperm are introduced through sexual intercourse.

fetus

In humans, an individual from eight weeks after fertilization until birth. A fetus that is near term is indistinguishable from a newborn except in certain physiological characteristics that change at birth, such as the closing of a blood vessel called the ductus arteriosus.

gamete

A haploid reproductive cell whose role is to unite with an opposite-sex gamete to create a new individual. Also called sex cells, they consist of eggs and sperm.

haploid

Having one copy of each chromosome per cell. In mammals, only gametes are haploid; all other cells are diploid.

implantation

The point at which an embryo, at the age of a few days in humans, becomes attached to the lining of the uterus.

in vitro fertilization

Fertilization that takes place outside the human body ("in vitro" literally means "in glass"). In vitro fertilization removes the sex act from reproduction. The zygotes are allowed to develop for several days into embryos, at which time one (or more) is placed inside the mother's body in the hope that it (or they) will undergo implantation, resulting in pregnancy. For practical reasons, it involves the fertilization of multiple zygotes, almost always more than can ever be implanted.

miscarriage

Also called spontaneous abortion, the unintentional termination of a pregnancy as a result of natural causes or, less commonly, accident.

newborn

Also called a neonate, an individual who has very recently been born. A newborn is indistinguishable from a late-term fetus except in certain physiological characteristics related to the loss of the placenta.

pregnancy

In mammals, including humans, the carrying of one or more embryos or fetuses in the uterus. In clinical terms, pregnancy begins at implantation, though the embryo exists as a separate individual in the mother's body before implantation. Thus pregnancy begins after the beginning of an individual human life.

sperm

A male gamete. In humans, sperm are small, motile cells that are produced daily in very large numbers by men's bodies.

stem cell

A cell capable of reproducing indefinitely, and usually capable of developing into one of several types of tissue. Stem cells are classified by "potency," that is, how many different types of tissue they can become. Stem cells are found in developing embryos, in umbilical cords, and in various other tissues such as bone marrow.

zygote

A brand-new, single-celled individual from fertilization until the first cell division, at which point it is called an embryo. The zygote stage in humans is very brief; it experiences the first cell division and becomes an embryo even before implantation.

The blog Science and Religion News, whose author Salman Hameed strongly favors science over religion, recently posted about two stories out of the Vatican. The post, entitled "Good Pope, Bad Pope," praised the pontiff for paying "tribute" to Galileo, but criticized him for the bioethics document Dignitas Personae.

"Good Pope": The Galileo Affair

In regard to the Galileo affair, it needs to be pointed out that the popular view — that Galileo was a noble pursuer of scientific truth against a scientifically backwards and rigid Church — is false. Galileo got in trouble for, in the words of Catholic apologist Jimmy Akin, being a jerk. Pope Urban VIII was actually sympathetic to Galileo's hypotheses about heliocentrism, despite being concerned that it would be difficult to work out the theological implications (which have since been reconciled with Scripture). He asked Galileo to explain, in Galileo's book Dialogue Concerning the Two Chief World Systems, the competing hypotheses of geocentrism and heliocentrism but not to advocate heliocentrism. Instead, the book ridiculed geocentrism and the pope himself, though there is controversy as to whether the apparent insults were deliberate or unintentional. It was the perceived riducule that got Galileo in trouble, not heliocentrism per se.

"Bad Pope": Dignitas Personae

In regard to Dignitas Personae, Hameed warns that in upholding previous teaching on bioethics (which asserts that all humans, including embryos, have certain rights, one of which I explained here), the Catholic Church risks becoming "irrelevant."

In other words, Hameed says that society as a whole will collectively dismiss the Church if she fails to accede to fickle public opinion.

This is the same Church that allowed the Protestant Reformation to become permanently entrenched in England over the indissolubility of marriage (in the Henry VIII affair). The same Church that suffered 400 years of prosecution in the Roman Empire for "irrelevantly" teaching that there is one God, incarnated in Jesus Christ, and denying the existence of the Roman pantheon. The same Church that has unblinkingly held to the "irrelevant" teaching that artificial contraception is an affront against God and against one's own spouse (a teaching consistent with the sublime Theology of the Body of John Paul the Great).

I'm laying my bets one who will be considered more irrelevant by history: the Church or the supporters of indignities against the tiniest humans.

Over at the Raving Theist, formerly the Raving Atheist, there is ongoing hubbub over the author's recently-announced conversion to Christianity. A recent post about conversion compared the conversion from atheism to theism, or conversion between different religions, to conversion between two philosophical schools of thought: empiricism and rationalism. I must admit that I had never thought too much about these metaphysical approaches.

One of the themes of this blog is that religion is rational. Clearly I am a rationalist. But I also am a woman of science, which necessarily makes me an empiricist.

The bottom line is that I cannot accept either philosophy as completely superior to the other. They complement each other. In science, purely empirical observations can only describe the world, not explain it. A rational approach is also necessary. On the other hand, science is meaningless without an empirical approach. A hybrid of the two philosophies, in which reason informs observations and observations guide reason, is best for learning about the natural world.

Another theme of this blog is that there are two distinct realms of truth, what Stephen J. Gould called the two magisteria: natural truth (the laws of nature, which are explored and explained by science) and supernatural truth (those parts of existence that are outside nature, meaning God and other non-material beings). In exploring the supernatural world, I favor rationalism as coming before empiricism. Empirical observations of the supernatural would include revelation (such as the Bible) and personal experience. These must be subject to the rational mind. The abundance of contradicting religious beliefs are evidence of what happens when one relies only on "empirical observations" of the supernatural without using the rational mind.

Some religions utterly rely on abandoning the rational intellect. If you have ever talked to Latter Day Saints missionaries, who encourage people to read the Book of Mormon and wait for a subjective fiffy experience to decide whether it is true, you know what I am talking about. ("Fiffy" means related to a "fif," or "funny internal feeling.")

What do you think is a better philosophy for looking at the world, empiricism or rationalism?

I enjoy Scientific American. I really do. So when it published an article on the newly issued document Dignitas Personae from the Congregation for the Doctrine of the Faith, I hesitated to comment here. It seems I so often criticize SciAm in this blog.

But then the secular pro-life blog Secondhand Smoke (hat tip to Der Wolfanwalt) made scathing remarks about the article, doing much of the job for me (and doing it better than I would have). So I really have no excuse not to make a few additions.

I am thunderstruck that when SciAm decided to interview an expert about a Vatican theological document, it chose a secular commentator, Josephine Johnston. This would be like interviewing an economist rather than a physician about a new recommendation by the FDA or the Surgeon General. And predictably, she makes both herself and SciAm look ridiculous by stating explicitly that she does not understand what she is talking about:

[The document] opposes IVF even if it doesn't involve embryo loss, because the Vatican is committed to conception that involves the conjugal act. This I don't really understand.

She does not understand it because she has no background in Catholic theology. But it stems from theological principles that underlie everything the magisterium has promulgated about sex and reproduction in the past 50 years. Dignitas Personae is completely consistent with Humanae Vitae, the landmark document that reaffirmed the church's opposition to artificial contraception, and John Paul the Great's theology of the body.

Johnston also sounds a little ridiculous at the end of the interview, when she says "I don't know enough about how Catholicism works in practice" and then implies that perhaps the Church should operate as a democracy when it comes to teaching. In theory and practice, Catholicism is not a democracy, but a Kingdom. Truth is objective regardless of fickle public opinion, and even if some members of the Body of Christ dissent, the whole of that Body will always be subject to his truth.

Way back in the day — say, a year or two ago — using search engines to research science topics was rather a crapshoot. I was an active Wikipedia writer back then, and the majority of my work was on science-related articles. And finding reliable web-based information was always challenging.

Take the article on the beautiful, endangered freshwater fish known as Asian arowanas, which is mostly my work (and I can't say I'm not proud of it). Google searches for Asian arowanas turn up mostly commercial sites and fan sites. Neither of these is a reliable source of science information: the commercial sites mix bona fide science with marketing information, while fan sites are prone to misinformation. This problem was a major hindrance to my work on the article.

Google search ranking

Now Google Search has a new feature for users signed in to their Google accounts: search ranking. (Try it.) Google says the ranking will help teach the search engine how to customize searches for you. Perhaps after some training, Google search will be less likely to turn up commercial sites and more likely to turn up useful research information.

But that will take time. In the meanwhile, two other search engines are available for people interested in finding real information on the web: hakia (still in beta) and Scirus.

Hakia, er, hakia

Hakia (whose name officially is not capitalized, but my inner English teacher just won't let me start a sentence that way) uses a new technology called semantic searching to help higher-quality, more credible sites show up higher in the search results, regardless of popularity. Other search engines, including Google, use popularity as a major criterion for search rankings; this is why SEO (search engine optimization) strategies include techniques like obtaining incoming links.

A script on the homepage allows a user to compare hakia and Google searches. I ran it for "Asian arowana." Hakia's top two sites were a fan site and a blog, while Google performed a bit better with the Wikipedia article and a commercial breeder's site. But a very significant difference between the two was visible on each page's right side: Google displayed an Adwords advertisement, while hakia showed a "hakia credible site": a journal article from the National Institutes of Health on the fish's mitochondrial genome. Hakia credible sites are those recommended by librarians, who know a thing or two about finding reliable information. Getting results like that "above the fold" is a huge advantage for the Web researcher.

Scirus

Scirus is billed as being "for scientific information only." It indexes journals, scientists' web sites, and other relatively reliable sources. In this regard, it is fundamentally different from both Google and hakia, which both cover the whole Web. So I compared it to Google Scholar, which searches academic journals.

My search for "Asian arowana" on Google Scholar turned up an unadorned list of various articles. The Scirus results, on the other hand, used logos to show each result's source at a glance. It also included a tool for refining the search. Scirus makes it easier to evaluate and filter search results. Its developers obviously understand the needs of a person looking for credible science information better than Google Scholar's designers do.

The first photographic images of exoplanets (planets orbiting stars other than our Sun) have recently been reported in sources including Scientific American, Space.com, and NASA. Exoplanets are typically discovered through indirect observation. Direct observation and photography of these worlds is notoriously difficult for a host of reasons: their tiny size (by definition, a planet must be smaller than even a dwarf star), their dimness, and their relatively close proximity to their parent stars, whose bright light drowns them out.

The image pictured comes from the University of California at Berkeley and depicts a planet orbiting a star called Fomalhaut. This composite image from the Hubble Space Telescope shows the planet's position in 2004 (bottom) and 2006 (top); from these data astronomers have calculated and graphed the planet's orbital path. Fomalhaut and its planet are relatively nearby, about 25 light years away.

Another amazing image consists of a system of three exoplanets, pictured at left, which have been detected orbiting a star with the unassuming name HR 8799. The Keck Observatory, which sits at the summit of Mauna Kea in Hawaii, claims the honor of creating these images.

There is a catch in calling these "the first" images, though. The devil is in the details, which not even many of the science writers reporting these images seem to have caught. As a matter of fact, at least two direct images of exoplanets already exist! I should know, because I wrote an article about them last month. One was taken as far back as 2004, and the other was reported (again, incorrectly as "the first") earlier this year. Oh, how quickly these science writers forget!

Neither the Fomalhaut nor the HR 8799 images are the first direct images of exoplanets.

As nearly as I can tell, the "firsts" for these images are this: the Fomalhaut images seem to be the first planet discovered through direct observation of visible light. The HR 8799 system images seem to be the first family of exoplanets discovered through direct observation of infrared light. The previously existing images I mentioned above, on the other hand, were discovered through the indirect methods that so far have been the main way of detecting exoplanets; the images were created only later.

All of these images are exciting. Planets outside our solar system intrigue the imagination! But please, I wish the science reporters would do a little fact checking and get their stories straight.

I had the misfortune finding an article by one Cynthia A. Janak on Gardasil, the vaccine against human papillomavirus. Though I would like to merely dismiss this article (oh, I so, so wish I could merely dismiss it), I am just too horrified by the heinous abuse of science. I cannot resist picking up poor Science, brushing her off, and patching her wounds a little.

I won't even address Janak's heavy use of anecdotal evidence. Instead, I'll focus on her attempt, starting about a third of the way down the page, to condemn Gardasil based on its "toxic" ingredients. She goes through the list one by one, quoting the horrible toxic effects of each ingredient:

• Gardasil contains 225 mcg of aluminum. Do you know how little that is? That's about 1/4000 gram, or less than 1/100,000 ounce. You get more aluminum eating out of aluminum cooking pots.
• Histadine is a substance found widely throughout the body. It can safely be taken daily in supplement form in amounts 2000 times greater than what is found in Gardasil.
• Polysorbate 80 is a type of compound commonly called a "wetting agent" and is found in ice cream and milk.
• Sodium borate is used to keep the pH balanced. Wikipedia flat out states that it "is not acutely toxic." You have to deal with very large quantities before you need to worry about safety precautions.
• Sodium chloride is table salt.

Did you notice that Gardasil also contains dihydrogen monoxide? You might like to read more about it here. I should warn you, though, that dihydrogen monoxide is just another name for water.

Janak's blog, Truthspace, is a manifestation of a mind deeply troubled by paranoia. The truth is that the first rule of toxicology is that the dose makes the poison. Cyanide, arsenic, and lead are all harmless in tiny enough quantities, while necessary substances like vitamin A, iron, and even water can be toxic in high doses.

Time may show that Gardasil is not a completely safe vaccine. I see no reason to make that assumption at this time. Gardasil may be a controversial vaccine, but not because it contains substances like table salt.

Poor Science. I hope she feels a little better now.

"Good" and "evil" are moral values that are defined in a metaphysical context of faith. In Christianity, "good" means that which is of God, and "evil" is that which is opposed to him; in fact, the words "good" and "god" have the same etymological root.

"Good" and "evil" are things we know not just with our minds or even our hearts, but with our spirits. A Christian would say that since they are spiritual concepts, they can never be defined scientifically.

What makes something evil?

What if you are a secular scientist who is nevertheless aware of the idea and existence of evil? You might do what artificial intelligence researcher Selmer Bringsjord, of Rensselaer Polytechnic Institute, did: try to define this non-scientific concept in scientific terms. Here are the criteria he came up with to define an evil person:

• The person must have planned or attempted (with or without success) to do something with the explicit intention of causing harm or pain to others.
• He or she must have done it without prompting, that is, independent of peer pressure.
• The person's reason for doing the morally bad thing must be either "incoherent," or the person must regard the harm caused as something good.

Compare these criteria to the three criteria that, according to Catholic moral reasoning, are necessary to make a mortal sin, that is, a grave evil that kills the life of Christ in one's soul:

• The act must be a grave matter — i.e., a serious wrong — or considered by the person to be a grave matter.
• The person must be aware that it is a grave matter — ignorance is an affirmative defense with mortal sins.
• The person must give full consent to the act without being coerced against his or her will.

These three criteria match Bringsjord's first two criteria rather well. Bringsjord's third criterion, though, seems superfluous or possibly even exonerating: if your reason for doing something bad is "incoherent," then you may not be sane and therefore not fully culpable for your actions; if you regard your evil act as good, you may fall into the category of people who are not aware they are committing a serious wrong.

Evil deeds v. evil people

One major discrepancy between Bringsjord's criteria and Christian views of evil stands out: Bringsjord is defining an evil person, while Christians talk only about evil acts. Traditional Christianity holds that all of us suffer from a fallen nature, so we are all inclined toward evil deeds; but because we were created in God's image to be with him, and because any sin can be forgiven, no human can be essentially evil. Thus the Church speaks of sins, not of evil people.

Why define evil with a secular world view?

What is Bringsjord's purpose behind defining evil people? He even created a computer model of a perfectly evil person — but to what end?

His model is part of a larger program of developing simulations for human behavior. If you have a wholly secular, materialistic worldview, and regard human behavior as the result of scientifically definable brain activities, perfect simulations are theoretically possible.

I would argue that Bringsjord is barking up the wrong tree. Moral decision making is dependent on the spirit, not just the organic brain. Computerized copies can never be more than approximations based on outward appearance; they will never capture the free will of the soul, which is involved in all choices having to do with good and evil.

Scientific American, whose articles often are noticeably skewed toward an antireligious (rather than merely secular) perspective, begins to make up for past transgressions with this fascinating profile on an accomplished geneticist and evolutionary biologist who speaks up for the compatibility of evolution and religion. Among the excellent points Francisco Ayala (who was once ordained a Dominican priest, though it's not clear whether he still practices any faith) makes:

• Evolution not only does not undermine a divine explanation for nature, it actually helps. It shows that the suffering in nature, caused by predators and parasites and plain bad luck, is amoral rather than immoral — that it is not evil in the sense of an act of the will. Since God by definition can do no evil, describing nature as neither good nor evil explains how a good God can create a world with natural suffering. It helps, in other words, with theodicy.
  
• Outside the United States, the strong feeling that "Darwinism" is the enemy of Christianity and vice versa is not prominent.
  
• The biggest reason I feel strongly about explaining how evolution is compatible with faith is reiterated by Ayala: Many intelligent Christian students of biology lose their faith when they discover the strength of the theory of evolution because they believe evolution and Christianity are incompatible. It is tragic to think of people turning from God as a result of learning more about his sublime creation.

Ayala's interest in the philosophy of science, unfortunately, does not seem to show as much evidence of his theological training as SciAm implies. For example, according to Wikipedia (admittedly not a terrifically reliable source), he has spoken out against the United States ban on federal funds for vivisecting human embryos.

Nevertheless, though I have far less education in both science and theology than Ayala, I would like to think that in at least some ways we are kindred spirits. We both oppose the sneering attitude of the "Brights" who think they have the corner on truth, when they are actually just closing their eyes to the brightest part of it.