Thursday, August 31, 2006

Casey Luskin Advances Agenda of Ignorance by Misappropriating Scientific Terms

Casey Luskin, of the contemptibly dishonest Discovery Institute, is bashing Jerry Coyne for saying:

“After lecturing this spring to the Alaska Bar Association on the debate over intelligent design and evolution, I was approached at the podium by a young lawyer. The tight-lipped smile, close-cropped hair and maniacal gleam in his eyes told me that he was probably a creationist out for blood. I was not wrong.” (Luskin’s emphasis)

in this book review found in Nature.

Luskin, who has more of a toothy smile but still has the characteristic maniacal gleam in his eyes ;), claims that the take home message from Coyne’s statement is:
b>“Don't ask hard questions about evolution of leading Darwinists, or you will get called mean-spirited names in major scientific journals.”b>

While noting that someone has a maniacal gleam in their eyes may not be nice, it’s certainly not calling them mean-spirited names.

Luskin then goes on to ask a bunch of rhetorical questions suggesting that anti-Creationist bias at Nature may be why they are unable to publish all their valuable research.

Other than completely ignoring this beautiful paragraph that is the actual take home message from Coyne’s review:
“In the end, the true value of evolutionary biology is not practical but explanatory. It answers, in the most exquisitely simple and parsimonious way, the age-old question: “How did we get here?” It gives us our family history writ large, connecting us with every other species, living or extinct, on Earth. It shows how everything from frogs to fleas got here via a few easily grasped biological processes. And that, after all, is quite an accomplishment.”


Luskin puts his own ignorance of science, or inability to keep his own metaphors straight, on display:

“Incidentally, one of the two commercial uses Coyne does find for evolution includes "the use of ‘directed evolution’ to produce commercial products (such as enzymes to protect crop plants from herbicides)." (pg. 984) "Directed evolution" is otherwise known as intelligent design.”(emphasis Luskin’s)


No Casey, directed evolution is not otherwise known as intelligent design. Here is the earliest reference to directed evolution (done in 1971) that I could find on PubMed:

DIRECTED EVOLUTION OF METABOLIC PATHWAYS IN
MICROBIAL POPULATIONS. I. MODIFICATION OF THE
ACID PHOSPHATASE pH OPTIMUM IN S. CEREVZSZAE’

J. C. FRANCIS2 AND P. E. HANSCHE
Department of Genetics, University of California, Davis,
California 95616
Manuscript received April 17, 1971
Revised copy received October 1, 1971
ABSTRACT

An experimental system for directing the evolution of enzymes and meta-bolic pathways in microbial populations is proposed and an initial test of itspower is provided.-The test involved an attempt to genetically enhance certain functional properties of the enzyme acid phosphatase in S. cereuisiae by constructing an environment in which the functional changes desired would be “adaptive”. Naturally occurring mutations in a population of I O 9 cells were automatically and continuously screened, over 1,000 generations, for their effect on the efficiency ( K , ) and activity of acid phosphatase at pH 6, and for their effect on the efficiency of orthophosphate metabolism.-The first adaptation observed, MI, was due to a single mutational event that effected a 30% increase in the efficiency of orthophosphate metabolism. The second, M2, effected an adaptive shift in the pH optimum of acid phosphatase and an increase in its activity over a wide range of pH values (an increment of 60% at pH 6). M2 was shown to result from a single mutational event in the region of the acid phosphatase structural gene. The third, M3, effected cell clumping, an adaptation to the culture apparatus that had no effect on phosphate metab-olism.--The power of this system for directing the evolution of enzymes and of metabolic pathways is discussed in terms of the kinetic properties of the experimental system and in terms of the results obtained.
What’s important to note about this process, directed evolution, is that the evolution occurs by completely random mutations. The end product, an improved enzyme, is not itself intelligently designed, only the selection process is designed by an intelligent agent. So if you’re trying to say that God the Intelligent Designer, created life and a system (natural selection) by which it was allowed to evolve through completely random mutations until present day biodiversity was established… Then fine, you’re a theistic evolutionist and a deist, not an advocate of Intelligent Design.

Nothing wrong with that, congratulations on joining the world of reason!

Unfortunately we all know you are a Creationist who tries to use science-y jargon and bad metaphors to try to make your beliefs seem to be based on evidence rather than Faith. That’s fine too, it’s a free country, but drop the misappropriation of actual science and scientific terms as belonging to, or supporting of, your Faith. It just puts your ignorance of science on display.
PZ Myers delivers a thorough lashing to the contemptibly dishonest Discovery Institute's David Berlinski for an erstwhile letter to Science.

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Saturday, August 26, 2006

Let Them Eat Jesus

National Council of Churches comes under fire from anti-Christian bigots.

Recently the 45 million person National Council of Churches has come under fire from a group called “Concerned Women for America” (CWFA) for encouraging its member Churches to support and actively work toward eradicating global poverty by fulfilling the United Nations Millenium Development Goals:

Goal 1. Eradicate Extreme Poverty and Hunger
Goal 2, Achieve Universal Primary Education
Goal 3, Promote Gender Equality and Empower Women
Goal 4, Reduce Child Mortality
Goal 5, Improve Maternal Health
Goal 6, Combat HIV/AIDS, Malaria and other diseases
Goal 7, Ensure Environmental Sustainability
Goal 8, Develop a Global Partnership for Development

Why would anyone attack the National Council of Churches for encouraging their members to support such goals?

Maybe the NCC is one of those pushy evangelizing groups that makes getting aid contingent upon conversion to Christianity?

it(the NCC-ed.) promotes harmonious relations among Christians, Jews, Muslims, Buddhists, practitioners of traditional Native American religion and many other faith groups in a society that is increasingly multireligious.”

No? Well then, perhaps Concerned Women for America is just one of those commie-pinko-liberal women’s Jesus-hatin’ groups?

We are the nation's largest public policy women's organization with a rich 27-year history of helping our members across the country bring Biblical principles into all levels of public policy.”

Oh! Guess not. Well then, what is the CWFA’s problem with the NCC's support of the UN?

The thesis of the National Council of Churches (NCC) booklet Eradicating Global Poverty1 is that for the first time in human history we have the ability to eradicate poverty and the way to do it is through the United Nations Millennium Development Goals. In other words, the NCC is saying that the United Nations, not Jesus Christ, is the salvation of the world.”

Ooo---kay.

The NCC is surrendering leadership to a secular entity
and offering utopian solutions, instead of Biblical ones, to the world's
problems. To add insult to injury, the NCC is using its member churches as foot
soldiers to carry forward the U.N. agenda around the world.”

Hmmm... Biblical Solutions huh? You mean like this one?


34Then shall the King say unto them on his right hand, Come, ye blessed of my Father, inherit the kingdom prepared for you from the foundation of the world:
35
For I was an hungred, and ye gave me meat: I was thirsty, and ye gave me drink: I was a stranger, and ye took me in:
36Naked, and ye clothed me: I was sick, and ye visited me
: I was in prison, and ye came unto me.
37Then shall the righteous answer him, saying, Lord, when saw we thee an hungred, and fed thee? or thirsty, and gave thee drink?
38When saw we thee a stranger, and took thee in? or naked, and clothed thee?
39Or when saw we thee sick, or in prison, and came unto thee?
40And the King shall answer and say unto them, Verily I say unto you, Inasmuch as ye have done it unto one of the least of these my brethren, ye have done it unto me.

http://www.biblegateway.com/passage/?search=Matthew%2025:34-46;&version=9;

Ok then, what else is wrong with the NCC program?

“ the NCC proposal substitutes a leftist agenda for
Biblical imperatives.”

But, but... Jesus said if we feed the hungry, we have fed him too, and we will be blessed. Wait,... does this mean Jesus was a leftist?
“The U.N. is actively anti-American; both the Security Council and the General Assembly work to thwart American interests.”

Ummm, I thought the NCC program is about eradicating global poverty, does feeding hungry people thwart American interests too?

” Perhaps the National Council of Churches and its member denominations ought to consider sending Christian missionaries into Haiti and other Third World nations; we just might see some transformed lives that would, in turn, transform communities and those nations. “

That sounds nice! Doesn't the National Council of Churches perform any mission work at all?

NCC member communion fined $34,000 for Cuba ministry

"We have had an ecumenical relationship with the Cuban Council of churches for a long time, as have churches and councils of churches around the world," President Bush's approval of these recommendations indicates that this administration is trying to dictate who our church partners can be and how our humanitarian agencies can deliver aid to people who need it. That is an incredible intrusion into free exercise of religion."

Well, I guess that answers my question about whether eradicating global poverty thwarts American interests. Or at least the Bush administration’s interests.

“Further, the goals of "gender equality" and "empowering women" include quotas and set-asides that are hugely problematic for Americans who believe in full opportunity for women, but who firmly oppose quotas and special treatment or exceptions.

From the UN Millennium Development Goals:

“...a world in which men and women work together as equal partners to secure better lives for themselves and their families. In this world, women and men share equally in the enjoyment of their capabilities, economic assets, voice, and freedom from fear and violence. They share the care of children, the elderly and the sick; the responsibility for paid employment; and the joys of leisure. In such a world, the resources now used for war and destruction are instead invested in human development and well-being; institutions and decision-making processes are open and democratic; and all human beings treat each other with respect and dignity.”

My goodness, that does sound hugely problematic.

OK Dr. Crouse can you show us some “brotherly love” for your fellow Christians and wrap all this up with a positive message?

Ah, such a nice little package of politically correct, utopian manipulation. Church groups around America can sit together and write up their ideas on newsprint for all the assembled participants to see. They can gather thoughts about calling members of Congress and they can feel good about their compassion for those who are less fortunate. They can increase the amount that they send to liberal organizations and encourage greater support for United Nations efforts. But I remind them of the remarks by the president of Haiti -- after 50 years of aid, there has been no noticeable improvement in that nation that has been the focus of so much U.N. attention. Pouring more money into a failed experiment won't bring better results.

So Dr. Crouse, what is your solution to global poverty?

”“The solutions are in mission work, where you send people to countries where they have never heard the gospel before and you break the cycle of poverty by offering people the hope of Jesus Christ.”

...

”Pouring more money into a failed experiment won't bring better results. Perhaps the National Council of Churches and its member denominations ought to consider sending Christian missionaries into Haiti and other Third World nations; we just might see some transformed lives that would, in turn, transform communities and those nations.”

Now I don't want to belabor the point that Haiti’s population is already 96% Christian... So I'll just note that in the effort to combat poverty:

  1. The United Nations has been around for 61 years.
  2. Christianity has been around for about 2006 years.

“Pouring more money into a failed experiment won't bring better results.”

--Janice Shaw Crouse, Ph.D

Maybe working together will?



**Concerned Women for America is an extreme right wing organization who opposes homosexual rights, reproductive rights for women including plan B, and has strong ties to the Bush administration best demonstrated by Dr. Janice Shaw Crouse being appointed as an official delegate to the UN despite her opposition to women's rights and her position as head of the Beverly LaHaye Institute whose anti-UN paranoia is most clearly demonstrated in the armageddon fantasies of the LaHaye's 'Left Behind' series. They're also closely associated with the "humanitarians" at Focus on the Family**

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Wednesday, August 23, 2006

Last "Rational" Reason for Opposing Embryonic Stem Cell Research is Gone

Anti-science opponents persist in objecting to research.

The last possible "rational" reason for opposing the funding of embryonic stem cell research has been removed. Newsweek reports that Advanced Cell Technology of California has published a paper in Nature's advanced online edition stating that their scientists have used a single cell extracted from a human embryo to produce embryonic stem cells. This procedure would allow the donor embryo to continue developing normally, thus acheiving the goal of creating embryonic stem cells without destroying embryos.



In the procedure, a single cell (blastomere) was removed from a donated embryo (a), the donor embryo was able to continue developing normally (b), the removed blastomere was allowed to grow overnight in the presence of human embryonic stem cells expressing a green fluorescent protein (c,d) (the green cells in d are embryonic stem cells used as feeder cells for the blastomere, and the cell with the arrow pointing to it in c and d is the blastomere derived cell) blastomere derived human embryonic stem cells grow normally (e).

The researchers envision their technique being used by families undergoing IVF to have children who want to have pre-implantation genetic diagnosis done to ensure that the implanted embryo does not carry a genetic disease. A single cell would be removed from the blastocyst and allowed to grow and divide separately producing cells that could be used for the establishment of embryonic stem cell lines as well as for pre-implantation genetic diagnosis.

Ten experiments were performed using sixteen donated embryos, resulting in 19 embryonic stem cell like outgrowths and two stable pluripotent embryonic stem cell lines. This success rate is similar to others in which the whole embryo is used to derive stem cells. These lines had the capacity to develop into all three germ layers.

a–g, Staining for markers of pluripotency, showing Oct-4 (a) and corresponding DAPI staining (b), TRA-1-60 (c), TRA-1-81 (d), SSEA-3 (e), SSEA-4 (f) and alkaline phosphatase (g). Scale bar, 200 m. h, Representative chromosome spreads of the two single-blastomere-derived hES cell lines. i, RT–PCR analysis of the expression of markers of pluripotency in single-blastomere-derived hES cell lines. Top panel, Oct-4; centre panel, nanog; bottom panel, GAPDH. Lane 1, no template; lane 2, negative control (MEFs); lane 3, MA01; lane 4, MA09; lane 5, WA01.

These lines continued to divide in an undifferentiated state for eight months.

However, as innovative as this procedure is, and in spite of the fact that it provides a method for creating embryonic stem cells without destroying human embryos, there is still opposition to this technique.

From the paper's author:
“Hopefully this will remove the last rational reason for anyone to oppose stem-cell research,” Lanza says."

Remove the last "rational" reason for opposing stem cell research? Yeah, I'd say we've reached that point by now. Let's see what other reasons there might be for opposing this research.

Falwell: Stem Cell Research 'Does Not Pass Smell Test'

...he said Tuesday that any medical research must pass a three-part
test: "Is it ethically correct? Is it biblically correct? Is it morally
correct?"
Stem cell research, Falwell said, "does not pass the smell
test."

(Editor's note: I don't know what Jerry Falwell's smell test is for stem cell research, but I hope I'm never asked to smell test Jerry Falwell! -- PhB)

"Richard Doerflinger, deputy director of pro-life activities at the
United States Conference of Catholic Bishops, says Lanza’s methods are
unacceptable for several reasons, including the fact that the experiments
leading to his recent advance—although done to develop a technique that would
preserve embryos—actually destroyed embryos in the process. “It does not solve
the ethical dilemma,” Doerflinger says. “It’d be irresponsible to claim now that
this is totally safe.”"


Unfortunately, in addition to overcoming whatever objections remain after the last "rational" objection has been removed, the President's completely irrational embryonic stem cell funding policy also stands in the way. This means that even though these lines were created without the destruction of a human embryo, they can't be approved for federally funded research because they weren't created prior to Ceasar's Bush's August 9, 2001, stem cell decree.

The company's supporters remain optimistic:

"I think this will become a standard way of producing stem cell lines," said
Ronald M. Green, a Dartmouth College professor of religion who is an unpaid
bioethics adviser to Advanced Cell Technology.The company, which has been
struggling financially, owns about 300 patents that it hopes to develop into
medical treatments.
After news of its announcement broke on Wednesday, the price of its over-the-counter stock shot up from 42 cents to more than $1.70 per share.

Although this procedure is completely foreseen by the company's previous work using mouse embryos it is useful for deomonstrating that there is no amount of back-bending, or hoop-jumping that will satisfy religious extremists who oppose scientific advancement.

Nature advance online publication 23 August 2006 doi:10.1038/nature05142;
Received 12 April 2006; Accepted 8 August 2006; Published online 23 August
2006
Human embryonic stem cell lines derived from single blastomeres
Irina Klimanskaya1,2, Young Chung1,2, Sandy Becker1, Shi-Jiang Lu1 and Robert Lanza1

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Tuesday, August 15, 2006

The Party of Sperm Worshippers

The Party of Sperm Worshippers!

THE REPUBLICANS, THE TWO-BIT WHORES AT THE CORNER, ANN COULTER,

AND THE DISREGARD FOR SAFE SEX


****COVER ILLUSTRATION REDACTED DUE TO BLOGGER’S RESTRICTIONS ON POSTING PORNOGRAPHIC IMAGES. SEE TERMS OF SERVICE.****


“The Reverend Timothy Tidwell, armed only with truth and logic, takes on George W. Bush, Ann Coulter, and that wanker Ramesh Ponnuru --and he’s the only one left standing.”

--John Stewart


Advance Praise for
The Party of Sperm Worshippers


"The power of this book is the force of its logic. Timothy Tidwell has given us the most significant statement on the need to worship sperm in America since Linda Lovelace's Deep Throat . Like Lovelace, he is calling America to return to its best self. And there is reason to hope that the country is listening."

--Leggy Noonan

"Timothy Tidwells's book will be accepted almost immediately as the seminal statement on human life. The Party of Sperm Worshippers is stunning as scholarship, ingenious in its construction, passionate-but never overbearing-in its convictions. It will be read for decades and revered as the most complete and resourceful essay on great questions that divide America."

-- William B. Fuckley, Jr

"Timothy Tidwell was once, like Ramesh Ponnuru, in favor of sperm wasting. Then he watched its logic unfold, was slowly repulsed, and then went over into resistance. His book, The Party of Sperm Worshippers, is an easily understandable account of the logic of sperm worship, from swapping to snowballing and beyond. This book cries out for mass-market sales in the hundreds of thousands, as the tide turns."

--Michael Nowank

"Thorough, heart-breaking, infuriating--an indictment that is also a cry for action by the people who still believe that sperm is the ultimate value."

--Cum Stain

Introduction

The Party of Sperm Worshippers started with vasectomies but its sickle has gone from threatening the ejaculated, to the nocturnal emission, to the condom confined; it has swept from the spank mag to the back seat to a generalized disregard for "inconvenient" human sperm.

Sperm wasting came to America because many Americans felt that in some cases it was the least bad response to a sticky situation. Only a small minority of Americans professed to have no qualms about sperm wasting at all, to see it as no different from a bowel movement.

Many more people were persuaded that it was better for a man to waste sperm than to resort to coitus interruptus. Advocates of sperm worship said that as many as one million sperm were being wasted every day of a teenage boy's adolescence.

Many people continue to support the legality of sperm worship for reasons like these. President Bill Clinton was politically astute in saying that sperm wasting should be "safe, legal, and rare"--a slogan that pointed back to the blue dress.

There was some self-deception in this resigned acceptance of sperm worship, and some plain old deception as well. American women weren't dying by the thousands becasuse of illegal sperm wasting. And pro-sperm wasting legislation seemed more modest than it was.

The Supreme Court ruled in 1973 that "emanations and penumbras" from the Constitution protected a right to waste sperm. The Constitution might not explicitly recognize the right, in other words, but it projected a shadow that protected sperm wasting. Monstrous things can happen in the darkness. In time, it became clear that sperm wasting had "emanations and penumbras of its own in our law, politics, and culture.

Science has shown us that every sperm has a little man inside.
All of us who read this page were once little men inside sperm. The history of our bodies began with the formation of a sperm. We were those sperm, just as we were once water, carbon, assorted organic molecules, and Calcium ions. The formation of the sperm marks the beginning of a new human life: a new and complete organism that belongs to the human species. Embryology textbooks say so, with no glimmer of uncertainty or ambiguity.*

*1. "In this text, we begin our description of the developing human with the formation and differentiation of the male and female sex cells or gametes,..." William J. Larsen, Human Embryology, 3rd edition.

2. Throughout history there have been several "answers" to the question of when human life begins, but the only consistency among the answers is that they are always changing as social contexts change, religious morals fluctuate, or new knowledge about the process of embryo development is obtained.” Scott F. Gilbert, Developmental Biology, Eigth Edition.

3. "It needs to be emphasiszed that life is continuous, as is also human life, so that the question 'When does (human) life begin?' is meaningless in terms of ontogeny." Ronan O'Rahilly and Fabiola Mueller, Human Embryology and Teratology, 3rd edition.

For a more serious look at Ramesh Ponnurus' new book The Party of Sperm Worshippers The Party of Death and why Ponnuru is completely wrong on the fundamental scientific issues in question, check out this review by the Reverend Timothy Tidwell.

Oh! If you're not offended yet, watch this video:
Every Sperm is Sacred Not Work Safe!

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A Review of Ramesh Ponnuru's Party of Death

The Democrats the Media, the Courts, and the Disregard for Human Life

(After President Bush’s veto of the Stem Cell Research bill I found myself wondering: What the heck are these people thinking? After reading “Party of Death” I have my answer. They aren’t thinking much, and they sure don’t know much about biology.)

”A foolish consistency is the hobgoblin of little minds, adored by little statesmen and philosophers and divines.”

Ralph Waldo Emerson, Self-Reliance

I am neither an expert on abortion nor a historian of law so, this being a science blog, I will focus on the portions of Mr. Ponnuru’s book where he draws on science to support his arguments. Because Mr. Ponnuru has presented a “secular” argument for the “Pro-Life” position based on his understanding of biological science, addressing his flawed use of science effectively rebuts most of his arguments regarding the beginning of life. (We’ll save end of life issues for another time.)

Briefly stated, Mr. Ponnuru’s position is that all living human organisms have a fundamental right to life that cannot be taken away from them. Thus, practices like embryonic stem cell research (ESCR), abortion, euthanasia, and physician-assisted suicide that cause a human organism to die are all violations of the fundamental right to life and are morally unacceptable.

In contrast to Ponnuru’s position is the fact that we all believe killing some human organisms is justified under certain circumstances; we just disagree about when and where such killing is appropriate. Ponnuru attempts to walk a tight-rope between justifying the killing of people during war or the death penalty, on the one hand, while maintaining that killing a zygote is evil on the other. He does this by claiming that viewing zygotes, blastocysts, fetuses, and the brain dead as non-persons sets us on a slippery slope that will lead us to accepting the killing of fully developed completely healthy people. It seems not to have occurred to him that by accepting the killings of civilians in war, or the execution of prisoners whom we fully acknowledge are people no slippery slope is necessary to lead us into accepting justifications for killing fully developed and healthy humans beings.

In Chapter 7 “The Politics of Personhood”

Ponnuru states that ESCR and abortion are

“...always choices to kill living human
organisms. We have developed ways of talking that enable us
to pretend that this point can be blinked away. In the case
of abortion and embryo research, the main technique is to suggest that there is
some great mystery about “when life begins,” and that this alleged question is a
religious or philosophical one. Yet science has long since
solved the mystery.”

Ah yes, science the great mystery solver! Mr. Ponnuru’s degree is in history. I wonder what an actual scientist would say on the matter?

When Does Human Life Begin?

This is a note that may generate some discussion and debate. It was occasioned by a bulletin board set up by a political action group at our college. The board claimed that while philosophy and religion may have different opinions concerning when life begins, science has no such problems. Students were told that biologists were unanimous in agreeing that life starts at fertilization, and that there was no dispute in the scientific literature. Besides being a parody of science (i.e., that scientific facts are the objective truth and that all scientists agree about what these facts mean), it is wrong. I have read a wide range of scientific positions on when life begins, and these positions depend on what aspect of life one privileges in such discussions.” (emphasis added.)



So apparently scientists are not quite as confident as Mr. Ponnuru that they have solved this mystery. Or, if they are certain, they disagree with him about what the answer is.


Mr. Ponnuru again:

“From conception onward, what exists is a distinct organism of the human species. The philosophical question is what we make of that fact. To jumble these issues together—the essentially scientific issue of categorizing an embryo as human and living, and the moral question of whether it follows from that categorization that it has a right to life—is a logical error.”

Mr. Ponnuru, this is precisely the logical error that you have made throughout your book, equating living organisms having human DNA with persons having rights. What’s more, you haven’t even applied this standard consistently denying entirely the rights of haploid Americans. Sperm and eggs being categorically human, living, and haploid organisms should, by your logic, have the same rights as a newborn child.

And here we come to the fundamental question in dispute. That question can be described in different ways: whether all human beings have a right not to be killed: whether membership in the human species is enough to confer rights; whether we accept the existence of a category of human non-persons. Opponents of abortion, embryo-destructive research, euthanasia, and infanticide believe that all human beings should be protected from being killed. They believe, further, that to the extent America fails to provide this protection it betrays its own founding principles. The party of death on the other hand, believes that some human beings deserve that protection and some do not.”

First, human being to me means person, a concept you have rejected so lets substitute another term you’ve used: human organism. We all believe that the killing of certain human organisms is justified and in the case of sperm and eggs, trivial. So if the “party of life” does believe that all human organisms should be protected from being killed they are going to have to make greater efforts to defend the rights of haploid Americans.

“All of us who read this page were once human embryos. The history of our bodies began with the formation of an embryo. We were those embryos, just as we were once fetuses, infants, children and adolescents. But we were never a sperm cell and an egg cell. (Those cells were genetically and functionally parts of other human beings.)”

While I agree that we were all once embryos, fetuses, infants, ... I find it impossible to believe that Mr. Ponnuru, or I, was never a sperm cell and an egg cell. I know that sex education is no longer allowed in schools these days but surely a man of Mr. Ponnuru’s age,... a graduate of Princeton,.... with a child of his own,... knows about the birds and the bees?

So why does he state that you, and I, and he, and everyone else who reads his book were never a sperm and an egg cell? His misguided notion that “Those cells were genetically and functionally parts of other human beings.” does not stand. Any student of biology will recognize that Mendel’s Laws of Independent Assortment and Random Segregation show that sperm and egg cells will differ genetically from the adult from whom they came were derived. As for “functionally parts of other human beings”, a sperm is certainly no more functionally a part of a man’s body than a fetus is functionally a part of a woman’s. So if a fetus is an independent organism living in someone else’s body, then surely a sperm is too.

Perhaps Mr. Ponnuru objects to the non-unitary nature of the sperm and egg prior to their union. But such a position would not accommodate the facts of twinning. We all know that an embryo can divide to form two or more individuals as identical twins, triplets, etc. But such a divided embryo can reunite to form a single unitary individual again. Surely Mr. Ponnuru would agree that such a ”reunited” individual is still a person, therefore how can the humanity of the un-unified sperm and egg be denied?

“The formation of the embryo marks the beginning of a new human life: a new and complete organism that belongs to the human species. Embryology textbooks say so, with no glimmer of uncertainty or ambiguity.”3

No glimmer of uncertainty of ambiguity?

Here Mr. Ponnuru earns points for including extended quotations from his citations in the notes, a practice he uses admirably throughout the book. However, upon examination, these notes do not strengthen his case. His own quotations from developmental biology textbooks refute his position!

“1) “In this text, we begin our
description of the developing human with the formation and differentiation of
the male and female sex cells or gametes, which will unite at fertilization to
initiate the embryonic development of a new individual” (emphasis added (by
Ponnuru)). William J. Larsen, Human Embryology,
3rd edition (Philadelphia: Churchill
Livingstone, 2001), p. 1. “

“We begin our description of the developing human with the formation and differentiation of the male and female sex cells or gametes...”

Why do you suppose we do that? It’s because life is a cycle, it is not a linear process with a beginning middle and end. Regarding the “...initiate the embryonic development of a new individual” yes, the zygote is a new individual, a new individual created from the fusion of two prior individuals: the sperm and the egg.

(I won’t even go into the fact that using an embryology textbook, a tome that typically deals with events post-fertilization to birth, rather begs the question of when life begins.)

Another citations reads:

(2)“It needs to be emphasized that life is continuous, as
is also human life, so that the question, “When does (human) life begin?” is meaningless in terms of ontogeny.”

And yet here is Mr. Ponnuru using this mans very words to justify his personal view of ontogeny, that human life/personhood begins at conception. To finish the quotation:

“Although life is a continuous process fertilization (which incidentally, is
not a moment) is a critical landmark because, under ordinary circumstances, a
new, genetically distinct human organism is formed when the chromosomes of the
male and female pronuclei blend in the oocyte”

I don’t think that anyone would disagree that fertilization is a critical landmark. But development is full of critical landmarks: spermatogenesis, oogenesis, gastrulation, neurulation, ....


Ponnuru knows the landmark he is looking for to signify the beginning of human life, and in his analysis he has set his sights on reaching that landmark alone, once there however Ponnuru refuses to inquire whether there is firmer ground further on or ground equally as firm elsewhere.

Ponnuru’s colleague at National Review Online, John Derbyshire, has identified the fundamental flaw with Ponnuru’s analysis of life issues, calling it “the Golden Rule of religious apologetics”:

The conclusion is known in advance, and the task of the intellectual is to erect supporting arguments. It would be an astounding thing, just from a statistical point of view, if, after conducting a rigorous open-ended inquiry from philosophical first principles, our author came to conclusions precisely congruent with the dogmas of the church in which he himself is a communicant. Yet that is the case, very nearly, with Party of Death. Remarkable!”

Ponnuru again:

The argument for the sanctity of human life is straightforward. If human beings have intrinisic dignity and worth, then they have this dignity and worth simply because they are human beings. It follows that all human beings have this dignity and worth. They are equal in the fundamental rights that attach to being human. These rights—and to have any rights at all must be to have a right not to be killed—cannot depend on particular qualities that some human beings have and others do not. They cannot depend on race, or age, or sex; <>nor can they depend on stage of development or condition of dependency.”

Nor can they depend on chromosome number or ploidy level Mr. Ponnuru. For example, male ants, bees, and wasps are all haploids. Aren't they still ants, bees, and wasps? Why would they be anything else? Sperm and eggs have human DNA and they are living. Therefore, according to your logic, they are entitled to the same rights as a ten-day-old baby.

“The party of death holds that there are no “human rights” in the sense of rights that come simply from being human. Rather, some human organisms have basic right because of qualities that they, in particular, happen to have; and those human beings who do not have these qualities are not persons with rights.”

Again, sperm and eggs are human. You have not acknowledged their basic rights in your book. You do not do so, I presume, because of certain qualities that they, in particular happen (not) to have, qualities that you yourself do have. Welcome to the party of death Ramesh!

I am reminded here of the age-old joke at the expense of scientists who find no need for God in the creation of life. A scientist goes to tell God that men no longer have any use for Him saying:

Scientist: “God, with our technology and science we no longer have any use for you.”

God: “But I created the Heavens and the Earth, I hung the stars in the firmament...”

Scientist: “No. With our science we’ve shown that the earth is just a planet revolving around the sun, and all the stars are just billions of other suns.

God: “But I created all life on earth.”

Scientist: “No, with our science we’ve shown that all living things arose through evolution, a completely natural process, there is no need for a supernatural Creator.”

God: “Ok. But can you do this?” God picks up a ball of clay, shapes it into a man and breathes life into it.

The scientist bends over to scoop up some clay.

God: “Ah, ah, ah,… You’ve got to make your own clay.”

Put to a similar challenge one can imagine Ponnuru attempting to create a “new human being” in a Petri dish, of course he has to start with two living human beings of a different sort from the one he wishes to create. This is the fundamental problem with the question:

“When does life begin?”

It doesn’t. Or at least it hasn’t, not in a very long time. Individual lives may end but all are connected to the same wellspring from which all life on earth has flowed. So we are not talking about human life beginning what we are talking about is individuation or personhood. This too is a continuous rather than a discrete process.

At the end of chapter seven Mr. Ponnuru reassures us that just because all human beings from conception until the grave have a fundamental right not to be killed that does NOT mean that we cannot kill people in wars or with lethal injections. Wheww!! That was close. For a second there I thought that whole “right to life” “Party of Life” “Culture of Life” might actually mean something. Thank God it’s just a tool for bashing your political opponents.

In Chapter 12 “Stem Sell: The Trouble with Ron Reagan”

Ponnuru attacks Ron Reagan Jr. for endorsing stem cell research at the Democratic National Convention. Ponnuru cites Rick Weiss’s article in the Washington Post quoting Alzheimer’s researchers as saying that treatments of Alzheimer’s using embryonic stem cell transplantation are not likely to work. This is an example of how opponents of ESCR distort the truth in order to hinder medical research. The fact of the matter is that embryonic stem cell research is expected to be very helpful in developing treatments for Alzheimer’s, not directly through stem cell transplantation, but by allowing researchers to create cells affected by Alzheimer’s.

"We may be able to create the disease in a dish. If we do that, we'll be able to better understand the disease and also to test drugs."

Ponnuru goes on to display further ignorance of embryology, stating that Ron Reagan “denies that the new biological entity created (by somatic cell nuclear transfer—ed.) is a fetus.” Of course it’s not a fetus it’s an embryo up to eight weeks which is far longer that cells would be harvested for ESCR. He claims that this is misdirection on the part of Reagan, I’ll make no claims about Ponnuru’s intentions, only note that he is completely wrong.

On Somatic Cell Nuclear Transfer (SCNT) or therapeutic cloning...

“The biotech industry, meanwhile, has gotten the state of New Jersey to pass a law authorizing human cloning for, among other purposes, the harvesting of “cadaveric fetal tissue” – in other words, the corpses of cloned fetuses.”

It should come as no surprise by now that not only is this not just an exaggeration by Ponnuru, it’s in an outright lie.

This bill does authorize the harvesting of embryonic stem cells from embryos created using Somatic Cell Nuclear Transfer. However, it also states:

“The bill stipulates that this research is to be: conducted with full consideration for its ethical and medical implications; and reviewed, in each case, by an institutional review board operating in accordance with applicable federal regulations.”

No IRB is going to approve “fetus farming”.

“If the goal is to generate healthy tissues that match a patient’s genetic profile, it seems circuitous to clone him, produce stem cells from an embryo, and then get them to generate the tissue. It would be much simpler to let the embryo grow to the point that it produced the tissues itself, and then take it apart.”

I agree with Ponnuru that “fetus farming” is not something we should engage in and, obviously, so did the New Jersey legislators. But there are cases where we would want cells, not organs for transplantation, for instance to treat spinal cord injuries. Clearly it is impossible to transplant the spine, but stem cells obtained from a therapeutically cloned embryo could be transplanted into an injured spinal cord and have been shown to heal spinal injuries in mice.

But it is disingenuous on the part of Ponnuru and his allies, to invoke the horror of fetus farming while maintaining their opposition to a bill that would impose a 10 year prison sentence and a $1 million fine as punishment for “implanting or attempting to implant the product of nuclear transplantation into a uterus or the functional equivalent of a uterus.”

S 1520

By opposing this bill in order to holdout for a ban on therapeutic cloning, the “Right to Lifers” leave the door open for groups like the Raelians or other unscrupulous entities to produce a cloned human being. Ponnuru actively endorses an incrementalist approach to banning abortions. Why does he eschew an incrementalist approach to banning cloning? As it is, their obstruction of a bill that would effectively end any attempt to reproductively clone a human being in this country leaves nothing between us and the bottom of the slippery slope but a gaping hole.

Overall, I saw little mention of birth control and no mention of Plan B in the book

Neither term appears in the index. In contrast, “partial-birth abortion” and D&X (the clinical abbreviation) do appear in the index as well as on pages: 38, 44-50, 56, 63, 211, 214; 47-48, 42-45 and 43-46, 56-57, and 63 respectively.

This seems a little odd given the recent opposition to birth control that has sprouted up among members of the “pro-life” movement.

http://www.salon.com/mwt/feature/2006/03/20/anti_contraception/index_np.html

http://www.usatoday.com/news/nation/2004-11-08-druggists-pill_x.htm

http://scienceblogs.com/terrasig/2006/06/pharmacists_emergency_contrace.php#more

It’s almost as if he wants to play up the most objectionable and disgusting procedures which are used by relatively few of his opponents, while trying to avoid arousing alarm about the his own group gradually forcing their beliefs on others. Given that Ponnuru has often endorsed an incrementalist approach to life issues, ie: overturn Roe v. Wade,--> pursue bans on abortion at the state level, --> further restrict access to contraceptives,--> ban in vitro fertilization,-->.... These omissions and the likely reason for them, brings up an interesting point.

Most hills have two sides. One man’s “incrementalism” is another man’s “slippery slope”.

If, as Ponnuru claims, the slippery slope on the side in favor of stem cell research leads to fetus farming, involuntary organ harvesting from people with mental disabilities, infanticide, involuntary euthanasia, and a long list of other horrors; where does the slippery slope on the other side of the hill lead? Bans on masturbation? Felonious menstruation? Mandatory mating? The Handmaid’s Tale? Every Sperm is Sacred?

I do give Ponnuru credit for at least trying to produce something worthy of rebuttal, as opposed to his former colleague at National Review and fellow Regnery author Ann Coulter, the rebuttal of whose book must have been as tedious as rebutting a collection of “dumb Pollock” jokes. But his refusal to embrace the full implications of the “pro-life” position cause me to doubt his intellectual honesty. And his misuse of science and attempts to vilify opposing points of view convince me that this is not an honest attempt to promote dialog, instead it is election year read meat being flung to the base, typical of the propaganda mill that is Regnery Publishing.

Update: Andrew Sullivan has the You Tube video of Ramesh Ponnuru on the Colbert Report.

Thursday, August 10, 2006

They Shall Take Up Serpents

"And these signs shall follow them that believe;
In my name shall they cast out devils; they shall speak with new tongues; They shall take up serpents; and if they drink any deadly thing it shall not hurt them; they shall lay hands on the sick, and they shall recover."


or not.

On Monday morning (Minister John-ed.) O'Kain was riding his bike through a wooded area near the camp's health center when he saw a thick-as-your-wrist rattler, maybe 3 1/2 feet long, sunning itself in the middle of the path.
...

"I figured the best thing would be to catch it and move it to another part of the mountain, away from the campers."

Good thinking Reverend O'Kain. You just pick up that snake, hop back on your bike, ride to the other side of the mountain, and let it go out of everybody's way. You're going to use your bare hands for that right?

He trapped it and was attempting to pick it up when it bit him near the nail on his right thumb. "It was more of a glancing blow with one fang, at first I couldn't even tell it broke the skin,"

A mere flesh wound.

Within a minute, his lips and face began to tingle.

Probably just the exertion from the ride.

Within three minutes, his arms and legs began to stiffen.

Lactic acid build up and muscle stiffness following an improper cool-down. Just need to walk it off...

In five minutes, his stomach began to cramp and he vomited.

Just something I ate.

In 10 minutes, his lungs and throat began to tighten and he had trouble breathing.

That's not good. Does anyone know how to "lay on hands"?
Emergency personnel gave him anti-venom medication. But because of his breathing problems, doctors had to also perform a tracheotomy. He was in and out of consciousness.

Well, at least he's not one of those guys who rejects science in favor of religious dogma.

Dr. Eric Lavonas, a toxicologist with Carolinas Medical Center, said O'Kain's reaction with breathing problems was extremely rare for a snake bite.

"Snake bites here in North Carolina are not rare. We average more than 400 a year, but mostly copperheads; we're ground zero for copperhead bites," said Lavonas, who also works with the Carolinas Poison Center. "It sounds that if without quick medical care, this man could have certainly died. We have only one or two deaths a year. He's lucky."


First, I'm happy that Reverend O'Kain is all right.

Second, no matter how good your intentions, never pick up a 3 1/2 foot long rattlesnake.

Third, I take this story as strong evidence that The Bible was NOT meant to be taken literally.


The only blog inspired by a Bumper Sticker.

These Are a Few of My Favorite Things

Raindrops in toilets and hemp skirts on hippies
Bright solar panels and shareholders’ yippees
Recycled newspapers tied up with strings
These are a few of my favorite things

Renewable fuels and turbines that spin in the wind
Caps on emissions and treaties we cannot rescind
Full spectrum sunlight from skylights in ceilings
These are a few of my favorite things

Cars emitting water instead of bad gasses
Americans on bicycles to work our fat asses
White healthy ice caps that don’t melt in the springs
These are a few of my favorite things

When the temp spikes,
When the storm stings,
When I’m feeling sad,
I simply remember my favorite things,
And then I don’t feel so bad.

There’s some good news in Newsweek discussing how large corporations and politicians are starting to see the need and indeed the value of sound environmental policies.
“Something weird is happening in the once marginal world of environmentalism. The green cause is no longer the preserve of woolly-minded liberals and fringe activists. Its tenets are being actively pursued by business leaders, stockholders and investment managers. In the popular mind-set, natural disasters such as New Orleans's Hurricane Katrina, floods in Eastern Europe and swirling desert sands in Beijing are now linked to a change in climate that threatens our way of life and our grandchildrens' future.”
Of course it’s the international version of Newsweek so the parties are largely European but many of the companies are multinational.

“The most startling turnaround, however, is among business leaders. Corporations are giving themselves green makeovers to improve efficiency, save money and look more attractive to investors and the public. According to a recent report from the Climate Group, an international environmental charity, 43 multinationals—including Bayer, BT and DuPont—saved a combined $11.6 billion last year by improving energy efficiency, reducing waste output and harnessing solar power.”

Unfortunately it seems like a lot of the exciting new ventures in alternative fuels that have entered the market recently are also foreign:

"The world's largest wind-turbine company, India's Suzlon Energy, was 28 times oversubscribed when it launched for $340 million at the end of last year. Chinese solar company Suntech Power raised $400 million in December; its share price has since shot up 50 percent. The largest venture-capital-backed IPO in Europe last year was of German renewable-energy company Q-Cells, which raised $400 million in October."
Lets hope that alternative energy doesn't become the next technology, after stem cell research, where Americans are going to be left behind

The only blog inspired by a Bumper Sticker.

Thursday, August 03, 2006

The 40th Edition of the Skeptic's Circle

is up at Daylight Atheism.

Some great selections:

The 2% Company on the absurdity that is homeopathy.
Oracs Friday dose of Woo: Mere Regularity is Not Enough.
And Eor's got a live wire in

Giant UFO Built Yowie Pyramids of Bullshit

an excerpt:
"Dian spontaneously accesses past life knowledge as a Master Sound Healer in the Court of Akhenaton in Egypt and combines it with vibrational knowledge from Higher Dimensions and Other Worlds."

Man, how come I never find anything that absurd?

The only blog inspired by a Bumper Sticker.

Figures

These Figures are intended to accompany this post. (A blogger bug prevented their posting contiguous with the text.)

Figure 1.



























Fig. 1. (a) Quarterly mortality rates and percentage of total patient-days receiving HAART among patients who ever had a CD4 cell count < style=""> Over 90% of HAART regimens were PI based. (b) Quarterly incidence rates of common opportunistic infections.

Figure 2.















Figure 3.

























Figure 4.























Click this image to enlarge.

Wednesday, August 02, 2006

"Skepticism" Run Amok, an Appropriate Level of Skepticism in Evaluating HIV/AIDS Causation

(This is a response from the virologist/epidemiologist who contributed this article.)

Thanks to both readers that have made it so far.

First: Michael is right. You can feel the rage dripping from his comments and are similar to those eloquently and bravely stated by my hero, the late Jonathan Mann, AIDS is one of the most important events in history, surpassing the Black Plague in its death toll . Measles, polio, meningitis, Kaposi’s sarcoma, obesity—almost every human affliction affects the poor and disenfranchised more frequently and more intensely. This is morally abhorrent. But distorting and denying facts will not help stop AIDS, even though we know that it is social conditions that allow this virus to flourish and to kill.

Second: George Lakoff is also right: don’t ever argue with the bad guys by letting them frame the debate. I knew that it was dumb when I did it, and I went ahead anyway.

Bialy puts up a series of silly questions that would deserve an “F” for any beginning student in an epidemiology course on causality. This isn’t just empty ad hominem pejorative as I hope to convince you below. But, I answered each question with cited research. Michael, anonymous, funkyfrankerbeany, etc. don’t attempt to address these studies and there is no evidence in their comments that they even read the abstracts. That’s not being skeptical, that’s just plain lazy (actually funk, when I was referring to swamp marsh gases, I was describing cholera, not malaria. The prevailing miasma theory for cholera was held until 1848 when John Snow, the father of infectious disease epidemiology, showed it to be bunk a London cholera epidemic and here). If you want to argue with me, bring your studies or stay home and stop wasting electrons.

The best and most eloquent single piece of evidence for HIV causing AIDS was cited in a posting on Dailykos.com regarding the infamous Harper’s article. Here is the logic: by the mid1990s, pharmaceutical scientists had developed protease and reverse-transcriptase inhibitor drugs designed on the properties of these proteins encoded by HIV. We are not talking about AZT, which was developed prior to the discovery of HIV, I’m referring to idinavir, nevirapine, etc. The reason why these drugs were developed and tested was solely their activity on the proteins that are made by HIV. If they affect the syndrome known as AIDS, and you still deny that HIV is a cause of AIDS, well, brother (or sister) I can’t help you. So what is the data for symptomatic AIDS in the era of these drugs? :


Or :

http://content.nejm.org/cgi/content/abstract/338/13/853

See Figure 2 here.

It is pretty clear from this graph what is going on across the US AIDS population once effective drugs that directly target HIV were approved and distributed in the US. This does not even begin to take into consideration blinded, randomized clinical trials (the gold standard for epidemiology) of each individual drug such as here, or here, or here.

So we see that antiHIV drugs are effective against AIDS on an individual level and on a population-wide level. Are some of these drugs outrageously expensive and do they have severe, potentially fatal side-effects? Yes, but that is another story and does not impact on whether or not HIV is the cause of AIDS, which in comparison has a near 100% fatality rate. To recap: 1) scientists identify key proteins encoded by HIV, 2) make drugs to specifically targeting these proteins, 3) treat AIDS patients who then have, 4) reduced mortality and morbidity of AIDS. Sounds kind of like HIV is causing AIDS, doesn’t it?

Sorry, can’t wrap my brain around the belief that the AIDS epidemic is all a surveillance artifact that we missed somehow in earlier decades before 1980 (hence HIV’s association with AIDS is an artifact). Having nine hundred thousand people keel over dead from diseases like Kaposi’s sarcoma, pneumocystis pneumonia and tuberculosis is pretty hard to miss (it could, however, be a conspiracy, see: Doctors'_plot). If the surveillance data that you see in these figures is AIDS, and if it is dropping on both population-wide levels as shown here and randomized, blinded clinical trials once HIV-specific drugs are given to patients, there are not very many other ways that you can interpret the data.

Bialy and Dean: I don’t see you as true skeptics, much as I would like to. Maybe this is just because I find your comments boring and incoherent. But, real skeptics would question the bases of these data and provide alternative explanations that might better explain them. A good skeptic should make these scientists really squirm. They might ask questions like, “What is the surveillance sensitivity?” What is the evidence that patients were truly randomized?” “What was the intent-to-treat effect?” These are reasonable skeptical questions and they are the types of questions asked every time a paper is peer-reviewed.

To me, it seems that “HIV-deniers” are the exact opposite of skeptics: they slavishly accept the hypothesis of Duesberg and ignore anything that disagrees with it—which pretty much includes all science generated over the past quarter century. Doesn’t sound like skepticism, sounds more like dumb.

Let’s talk about chimps and AIDS since the Bialy crowd is fixated on this, although I don’t know why. This gets back to the species specificity issue--which isn’t very interesting, I would pick a better argument if you want to deny that HIV is the cause of AIDS. Viruses, having evolved over thousands to millions of years, have genetically aligned themselves with their hosts. A reasonable skeptic always asks “Does the disease in an animal model truly represent the same pathogenic process in humans?” Personally, I find infecting chimps with anything immoral because of their high degree of social and behavioral sophistication. But they are infectable with HIV. They tend to not develop full AIDS syndrome but this hardly falsifies HIV as the cause of AIDS. In fact, HIV is a zoonotic infection spread to humans of a chimpanzee virus from the subspecies Pan troglodytes troglodytes. Beatrice Hahn and her coworkers have done brilliant work in figuring this out. There are four major subspecies of chimps, and she showed that one of them is the natural host of HIV. P. troglodytes troglodytes have widespread infection with HIV and the obvious conclusion is that chimpanzees and HIV have genetically adapted to each other and the virus does not cause symptomatic disease in this primate. Regardless of your interpretation of this data, lack of AIDS symptoms in chimpanzees after HIV infection is not a useful argument (see story about African and Indian herpesviruses).

Alright, so I addressed Bialy’s questions, now it is my turn. How do scientists determine causality? The single best and most accessible article on this is here.

I don’t agree with Fredericks and Relman on everything they say about causality but it is masterful and should be read by everyone who is interested in the subject. I go further--you shouldn’t post on a blog about HIV and AIDS causality without reading it, it is that good.

David Hume (1711– 1776)


Causality is an area bridging science and philosophy. One of the first people attempting to address this question was the Scottish empiricist, David Hume who had many interesting ideas. First, he said we cannot state causality by reasoning alone and it must rely on empirical observation. This is true even for mathematical causality, an area where pure reason might apply and is seemingly an ideal case for causality through sheer reason. Principles used to secondarily derive causal inference are based on axioms derived from observation (e.g. 2 plus 2 causes 4. Okay, but what is a 2? Well, we see one thing and another thing just like, and we call them two. We are defining “two” by our experience). Although, this may seem obvious, it overthrew a line of Aristotelian thinking that held sway over 18th century science and is still in vogue with Duesberg. Secondly, as described here:

When we examine experience to see how expectations are actually produced, we discover that they arise after we have experienced "the constant conjunction of two objects;" only then do we "expect the one from the appearance of the other." But when "repetition of any particular act or operation produces a propensity to renew the same act or operation...we always say, that this propensity is the effect of Custom" (EHU, 43)” Morris, William Edward, "David Hume", The Stanford Encyclopedia of Philosophy (Spring 2001 Edition), Edward N. Zalta (ed.).

In essence, if B always follows A, then we say that A causes B. This is short-changing Hume’s ideas but it illustrates the point.

See Figure 3 here.

Graph illustrates problem of saying that if B is always associated with A, then A causes B.

Unfortunately, life is rarely this simple and it is easy to make logical arguments against this definition of causality. For example the epidemiologic concept of confounding (a reasonable, but not perfect, explanation of confounding is here) is problematic for this:

one ruse perpetrated by tobacco companies was that it was not cigarette smoke that causes lung cancer, it was the sulphur smoke from matches that caused lung cancer. How do you separate the two? Well, this requires a study in which you recruit sufficient numbers of lung cancer patients so that a large enough fraction only used zippo lighters (by the way this reminds me of a superb piece of music by Phil Kline called Zippo songs here and here) so that you can show that folks who did not use matches but smoked cigarettes still developed cancer. You can see that it is pretty easy to trip up an epidemiologist and that it is really tough to prove causality.)

In the realm of infectious diseases, the next major player to address causality was the German microbiologist Robert Koch (pronounced like you-know-what, not like the soft drink). Koch is considered the “Father of Microbiology’ (actually co-Father along with Louis Pasteur and the two despised each other). Koch not only defined anthrax, discovered cholera bacteria and the bacillus that caused tuberculosis, he also asked the question “How do I know that the organism that I’ve found, actually causes disease?” Koch’s postulates are as follows:

  1. The agent is always present in the case of disease (see Hume above).
  2. The agent is never present in the absence of disease.
  3. The agent induces disease in a susceptible host.
  4. The agent can be isolated in pure culture again, and introduced into a new host, causing disease.

This was a brilliant construction appropriate for the 1880s, but I would no more have Koch be my causalist than I would have Sigmund Freud be my psychotherapist. Unfortunately, eager biology freshman are still tortured with these postulates and it is no wonder that they don’t want to become scientists. Koch did not know about asymptomatic carrier states (people are infected but don’t have disease such as with the bacteria causing meningococcal meningitis and can pass it on to others, but very few actually have disease), and he did not know about viruses (discovered by Dmitri Iwanoski in 1892. Koch did a great job, like Hume before him, but biology and life ain’t that simple.

Often you will hear the MIGHTY ROAR: NO ONE HAS PROVED THAT HIV FOLLOWS KOCH’S POSTULATES!!!! Whoa, got me there, you clever guys! The reason is that you cannot isolate a virus in free culture the way that Koch had in mind for bacteria. So, by the same reasoning, no one has proved that any virus has ever caused disease. Some people have tried to manipulate Koch’s postulates around by examining cases where HIV was transmitted through blood transfusion as an example of transmission of an “isolated agent” but it doesn’t really work well and I agree with Peter Duesberg that this is pretty twisted logic. It isn’t what Koch meant, so heed the advice of Lakoff and don’t even try to define modern causality in terms of Koch’s postulates.

Enter Austin Bradford Hill and Richard Doll.

  1. Association
  2. Generalizability
  3. Temporal Relationship
  4. Specificity
  5. Biologic Gradient
  6. Coherence
  7. Biologic Plausibility
  8. Experimental Evidence

Hill and Doll are largely credited (appropriately so) for describing the relationship (i.e., cause) between lung cancer and smoking. This was again a brilliant period for epidemiology, they developed and expanded technical methods such as case-control studies, cross-sectional studies, and cohort studies that are the bread and butter of epidemiology. Since we can’t ethically experiment on people (to cause severe illness or death), how do we take the existing data that we do have on the natural history of disease to make causal inference?

Epidemiology is fundamentally different from experimental science. Epidemiology, like astronomy, is an observational science. We have to take the data that we have and analyze it, so that we can tease apart associations and figure out the most likely explanations for what the underlying mechanisms are for how patterns of disease occur.

In terms of HIV and AIDS, we see a syndrome that we call AIDS (won’t belabor what this is, look it up here), we see certain people getting AIDS. Who are they? What is similar about them? What is different? We also find a new retrovirus called HIV. Who is infected with it? What happens to these people? Is it the cause of AIDS? How do we know?

Bradford Hill came up with a set of “criteria” which are really common-sensical. He said the following (more or less) that if an agent (cigarettes, HIV, etc.) causes disease (lung cancer, AIDS, etc.), even in this messy world it should have the following characteristics:

Association: The agent should generally be found associated with disease.

This is what Hume said. Even Duesberg et al. agree that AIDS patients are generally all HIV+. They just say that it is a passenger virus that doesn’t actually cause disease. So read on.

Generalizability: The agent should be associated with disease in different settings, by different people using different methods and so forth. Yep, HIV is seen in US AIDS, African AIDS, AIDS in old people, AIDS in young people, AIDS in red people, AIDS in blue people, etc. Okay, Peter is still with us here.

Specificity: The agent should be generally associated with just one disease or only a few diseases. This is like Koch’s second postulate but a little less strict. Hill thought this was the weakest piece to causality because it is clear that cigarette smoking not only causes lung cancer, but also emphysema, head and neck cancer and so forth. But the point is that if you postulate that an agent causes every kind of disease then you can’t prove that it causes any disease. Oxygen is always present in lung cancer. Does oxygen cause lung cancer? Maybe, but you can’t prove it so why worry about it. So, the number of diseases associated with the agent should be limited and the more limited and precise they are, the more likely the agent causes these diseases. In particular, if the diseases tend to be linked to each other and people who get one of the diseases also gets others (as lung cancer, emphysema, head and neck cancer are) then the association is specific.

Here’s where we lose old Pete. He seems to think that HIV is a harmless virus that coinfects AIDS patients who are sick for other reasons. In other words, HIV is not specific for AIDS. If Peter D were right, lots of people would have HIV but would not have AIDS or symptoms that a reasonable person would think are a prelude to AIDS. Fortunately, HIV infection is very uncommon in the United States and only about 0.1-0.3% of people have this virus. So, not a large percentage of Americans are running around with asymptomatic HIV infection.

What happens to people that are infected with HIV? Unfortunately, HIV is an uncommonly vicious virus and most if not all people infected with HIV eventually develop AIDS. Rutherford and colleagues followed a group of 489 gay and bisexual men who had been infected with HIV by the early 1980s . They followed this group for 11 years, when 46% had developed AIDS, and another 43% had “preAIDS symptoms” (e.g. swollen lymph nodes, dropping CD4 cell counts, etc.) More importantly, when they plot the rate that people with HIV get AIDS, it looks like the incubation period is very long, about 10 years but there is no evidence that a large fraction of people are protected from getting AIDS. This means that it looks like almost everyone with HIV, if left untreated, will develop AIDS. This is very different from most infections. The bacteria that causes meningococcal meningitis, for example, is present in the throats of about 10% of us at any one time but the chances of getting meningitis are small (about 3 per 100,000 people per year). Similarly for the virus that causes cervical cancer: many women are infected at one point or another, but only a small fraction develop cancer. Not so with HIV. So on the basis of this alone, it is very striking that HIV is causal for AIDS. But let’s go on….

Oh wait, says Duesberg and Bialy, people with AIDS have many, many diseases! This also violates your specificity rule! Let’s think about this for a second. AIDS patients have one fundamental underlying disease: their immune system is crapping out. This means that they secondarily get lots of different infections but the underlying commonality is that they all have severe immunosuppression. You do not find people with AIDS who have an intact, healthy immune system. So, if you define disease this way, which makes a lot of sense, HIV is very specific. If you wanted to be as pedantic as Pete D., most lung cancer patients don’t die of lung cancer either. They die of septicemia (overwhelming infection), pneumonia (infection of the lungs), respiratory failure, cerebral bleeding (from brain metastasis), liver failure (from lung metastasis), etc. Get the pikshur?

Dose-response (also Biologic-gradient): The more someone is exposed to an agent, the more likely that they will get sick with the disease. This makes a lot of sense for environmental exposures like cigarette smoking (a 40 pack-year smoker is more likely to get lung cancer than a 15 year old who steals his Mom’s Marlboros, lights up, gets green-sick and never touches cigarettes again). But it isn’t so good for infectious agents like HIV, since these agents replicate. Getting infected with one virus will get you as sick as getting infected with 10 viruses. So this is sometimes interpreted as, do we find the agent at the site of the disease and less so in more distant sites?

For HIV, this would be in the lymph nodes and thymus where CD4 cells live and that is precisely where the virus is found. So, what’s next?

Temporal Association: This was Hill’s key criteria, the big enchilada. I f an agent causes disease then it MUST precede the presence of the disease. If it doesn’t, then it would be a passenger virus, as Duesberg suggests. There are many, many cohort studies showing seroconversion to HIV and then subsequent development of AIDS. Go look them up. It is good mental exercise for you and I’m getting tired of doing your heavy lifting. HIV infection does not come after AIDS. Just doesn’t. Do an internet search using the terms “cohort study” with “AIDS” or “HIV”. I recommend PubMed.

By the way, technically this is the very most difficult thing for epidemiologists to determine. The reason is simple math: if someone develops a disease at a rate of 1 case per 1000 people per year (a very common disease, most diseases including AIDS are less common), you would need to follow 100,000 people for a year or 1000 people for 10 years to see only 100 people develop disease. Very expensive, and tenure committees rarely let you sit on your hands for 10 years until you collect your data. If you are looking for uncommon associations, then it can be very hard to see them this way although it is the best way. This is called a cohort study. Because cohort studies are really tough, most disease are studied by collecting disease cases (that could come from populations of millions of people) and then comparing them to control healthy persons. This is called a case-control study.

What’s next? Biologic Plausibility: Hill thought that for an agent to be causal for disease, it should make biologic sense that it is capable of doing so. For example, some people are concerned about electromagnetic (EM) radiation from electric poles causing cancer. Biophysicists tell us that this EM radiation is several orders of magnitude too weak to break DNA molecules, causing mutations and therefore cancer. This doesn’t mean that EM radiation does not cause cancer, it is just as of right now there is no biologically plausible mechanism to explain how it could do this. So this is strike against EM causing cancer unless science comes up with a plausible explanation of how this could occur.

Duesberg cites this for HIV as well. Once upon a time in the 1970s, he was a respected retrovirologist (which he and his followers will pummel you with if you let them). He hasn’t done any significant work in the field for nearly 30 years but when he was a cracker-jack, he was right, there weren’t a lot of other retroviruses that could cause diseases like this. But surprisingly enough, science has progressed since 1975 and indeed there are viruses like SIV/HIV-2, which have been found to behave similar to HIV in causing immunosuppression in monkeys and in people. Most of Bialy’s silly questions wash up on the shore here of biologic plausibility and were addressed in my previous comment. Interestingly, biologic plausibility is a minor criteria for causality, and Bialy seems likely to be unaware of Hill’s other major criteria as outlined above.

Epidemiologic coherence: By this, Hill meant, when taken together does all the data make sense? So if HIV were common in South Africa (which it is) but there was no AIDS there, it would not make sense. Gay, bisexual men, intravenous drug users and hemophilics have high HIV rates. Guess what? These are the same groups in the US who have high rates of AIDS. Think of any group, condition or incident and the patterns of HIV infection and AIDS follow each other.

Experimental data: As epidemiologists, we don’t experiment on people, do we? Actually, we do. There is a study design called a clinical trial where you take a group of people, randomly pick half and treat them one way, and either don’t treat the other half or you treat them in another way. Then you find out if they have different outcomes. A blinded trial is where the investigator is purposely kept in the dark as to who is who, until the study is finished. Then the identity of who got treatment A and who got treatment B is compared to their clinical outcome. This is precisely what was done to determine the effect of neveripine, etc. as described above. This is actually a very, very strong piece of evidence if you have a drug or vaccine that can target an agent such as HIV. Since the participants are randomly assigned to receive the drug or not, this evens out differences between individuals if a large enough group is studied.

Phew, okay so that is how scientists have and do determine causality. That was a long one. Still with me? The big point here is that Hill was not dogmatic. He didn’t say you had to have all of these criteria exactly nailed to say that an agent is causal for disease (although they are nailed cold for HIV and AIDS, case closed and has been closed for nearly 20 years). He used a lot of modifiers and adjectives, like “should be associated”, “often is present”, “usually is the case” and so forth. Why? Because the real world is messy and people are messier. Sometimes they lie, sometimes tests are a little inaccurate, sometimes the epidemiologist is an idiotic and mislabels something. Or sometimes people use PCR. Also, notice, that causality cannot be determined by one, single study because no matter how good it is, it won’t have been validated by multiple investigators and thus violates the generalizablity rule.

So, not all studies will be perfectly concordant and not all data will perfectly point to a cause. A.B. Hill was smart enough to realize this. You are suppose to interpret the data, not simply regurgitate it! So, if when you look at all of the different studies on HIV and AIDS, you have to ask how many studies support each one of Hill’s criteria and how many don’t? Can they all be logically reconciled in an unbiased and fair way? Are there studies that are so bad, so stinkeroo (a technical epidemiologic term), that they should be ignored?

Okay, now that you know how scientists approach questions of causality, I’m going to get really perverse. At a more fundamental level, causality is relative. Yes, that’s right, I’m about to throw out everything I said above. Does having unprotected anal intercourse cause AIDS? Yes, but only if the insertive partner is HIV. Does having receptive any intercourse with an HIV positive partner cause AIDS? Yes, but only if you don’t have a specific CCR5 allele, and so forth. For every disease there are a series of causal links. For infectious diseases such as AIDS, these links include the agent (e.g. HIV) but not exclusively. So at a fundamental level, when Michael says that poverty, racism and homophobia cause AIDS, he is absolutely right and a properly designed epidemiologic study can measure these things.

With the possible exception of rabies virus, HIV/AIDS is actually the most clear case where the virus alone is causal for disease. For just about every other infectious disease the case for proving a causal relationship between the agent and the disease is much, much foggier. Epstein-Barr virus (EBV) was discovered in 1964 (hmmm, Epstein-Barr virus was actually found by Epstein and Barr--and Achong who was an excellent Ghanaian scientist but who was conveniently left off of the name the virus. Don’t want to be too facile about racism but this is pretty damning. Barr’s first name is Yvonne so at least sexism wasn’t also at play) in an African lymphoma called Burkitt’s lymphoma. After 42 years, there are still people arguing about whether or not EBV causes Burkitt’s lymphoma. It does, but that is another story. The point is that most infections are asymptomatic and never cause disease. Other risk factors, such as nutrition, previous immunity from related viruses, and so forth, actually determine whether a person develops disease once they are infected. So, these other noninfectious factors are causal for disease as well. HIV is unusual and unusually bad since it seems like to cause disease in a much higher proportion of people infected compared to other viruses.

Now there is a second thing that epidemiologists do not like to talk about: Hill’s criteria for causality are BIASED. They are based on pathoepidemiologic assumptions. The easiest way to see this is the dose-response or biologic gradient criteria. Here he assumes that an agent will be either more likely to be at the site of disease than elsewhere, if the agent causes disease. But, what about a virus or bacterium, let’s call it Agent X, that causes an autoimmune disorder? What if the disease manifestation is results because someone’s immune response is too good and they not only get rid of the invading organism, but they also start attacking their own cells? In this case, the opposite of Hill’s dose-response criteria would occur. People who are sick because of Agent X infection will paradoxically have lower rates of prevalent infection with Agent X than healthy controls. Yeowhhhh!!!

It is possible we will find new infectious agents that cause disease in ways that we haven’t previously thought of. But once these mechanisms are figured out, Hill’s criteria may not be appropriate anymore.

Here comes the third piece of heresy: causality is normative. If you go through Hill’s criteria there is no magic point at which an agent is proven to cause disease. In fact, you can never prove an agent causes disease. You can only prove that it does not. So, eventually enough smart people who know enough about all the evidence, eventually start to say, “hey, guess what? HIV causes AIDS”. And the rest of the world believes them. That’s it. So Peter Duesberg is right: there is a big conspiracy and all of the scientific community and all the physicians are in on it. Drug companies, too. White House as well.

Now that we know something Duesberg doesn’t know, which is how to determine a causal relationship, let’s beat Peter to the punch and steal his thunder.

Come on, just shout it out: “They say that HIV causes AIDS but they C-A-N-N-O-T prove it!” And, truth be told, Duesberg is right and anyone who has seriously thought about the issue knows it. We also cannot prove that poliovirus causes polio, Corynebacterium diptheriae causes diptheria, Bacillus anthracis causes anthrax, etc, and we cannot prove that HIV causes AIDS. Can’t be done so that everyone in the world including Peter Duesberg and his ilk will believe it. The reason is because causality is normative and at some point intelligent people weigh all of the evidence for and against a causal relationship and then they decide. But there is one truth that my medical resident taught me in medical school: “Stupidity is an incurable disease”, and there will always be a far right portion of the bell curve that won’t believe that HIV causes AIDS. But if it saves millions of lives by treating HIV-infected people with antiretroviral drugs and developing a vaccine to stop this pandemic, well, I’m willing to fudge a little and say that HIV causes AIDS.

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