The Blinne Blog

Computer Games Can Save Your Brain

If you're one of the many people who while away hours playing FreeCell, that heinously addictive and complicated version of Solitaire, you may be interested to hear that some researchers think your performance in this computerized card game might reveal early signs of dementia.


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Despite Bush Veto Stem Cell Research Abounds

It seems that people believe that if there is no federal support for research using new embryonic stem lines then all stem cell research in the U.S. is at a standstill. This article shows that this is not the case.

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Food Crop Biofuels Given Thumbs Down By National Academy of Sciences Study

Producing biofuels such as ethanol from food crops isn't worth the effort a new and painstaking study published this week in the Proceedings of the National Academy of Sciences. Researchers should instead concentrate either on producing ethanol from indigestible plant material such as cellulose, or on synthetic hydrocarbon fuels.

read more | digg story

Autistic or Just Geek?

I have a son who is autistic and a number of my engineering friends are autistic. Digg.com is commenting on a Wired article that encourages techies to take an autism test.

My comments on digg follow.

While it is true that technical people have latent autistic tendencies, tests like this promote over diagnosis of the problem. Here's a recent news article from the journal Science:

If cases of autism are on the increase, as some believe, here's one provocative explanation: Blame the rise on marriages between like-minded people, whom psychologist Simon Baron-Cohen of Cambridge University in the U.K. calls "systemizers."

Baron-Cohen argues that autism and related conditions like Asperger's are manifestations of what he calls the "extreme male brain": one with weak social skills and a strong tendency to "systemize," or think according to rules and laws. In a study of 1000 U.K. families, he has reported that the fathers as well as the grandfathers of children with autism spectrum conditions are more likely to work in professions such as engineering. And the mothers are also likely to be systemizers "with male-typical interests," he says.

Baron-Cohen, whose theory is in press at the journal Progress in Neuropsycho-pharmacology and Biological Psychiatry, says he and colleagues are performing genetic studies, collecting subjects, and conducting population surveys in systemizer-heavy areas, such as Silicon Valley, to test the idea that techies marrying each other is raising autism rates.

Some balk at the idea. Psychologist Elizabeth Spelke of Massachusetts Institute of Technology says there's no good evidence for an "inborn, male predisposition for systemizing." But psychiatrist Herbert Schreier of Children's Hospital in Oakland, California, believes the intermarriage of techies "probably does account for why you have pockets of high autism around Stanford and MIT." Drawing on his own practice, he adds that fathers of children with learning disabilities have a disproportionate tendency to be engineers or computer scientists.

My son and a number of my technical friends' children do have autism spectrum disorders. BTW, here's the real test from DSM-IV which was the criteria for my son's diagnosis:

DSM-IV Criteria, Pervasive Developmental Disorders 299.00 Autistic Disorder

A. A total of six (or more) items from (1), (2), and (3), with at least two from (1), and one each from (2) and (3):

(1) qualitative impairment in social interaction, as manifested by at least two of the following:

(a) marked impairment in the use of multiple nonverbal behaviors, such as eye-to- eye gaze, facial expression, body postures, and gestures to regulate social interaction

(b) failure to develop peer relationships appropriate to developmental level

(c) a lack of spontaneous seeking to share enjoyment, interests, or achievements with other people (e.g., by a lack of showing, bringing, or pointing out objects of interest)

(d) lack of social or emotional reciprocity

(2) qualitative impairments in communication, as manifested by at least one of the following:

(a) delay in, or total lack of, the development of spoken language (not accompanied by an attempt to compensate through alternative modes of communication such as gesture or mime)

(b) in individuals with adequate speech, marked impairment in the ability to initiate or sustain a conversation with others

(c) stereotyped and repetitive use of language or idiosyncratic language

(d) lack of varied, spontaneous make-believe play or social imitative play appropriate to developmental level

(3) restricted, repetitive, and stereotyped patterns of behavior, interests, and activities as manifested by at least one of the following:

(a) encompassing preoccupation with one or more stereotyped and restricted patterns of interest that is abnormal either in intensity or focus

(b) apparently inflexible adherence to specific, nonfunctional routines or rituals

(c) stereotyped and repetitive motor mannerisms (e.g., hand or finger flapping or twisting or complex whole-body movements)

(d) persistent precoccupation with parts of objects

B. Delays or abnormal functioning in at least one of the following areas, with onset prior to age 3 years: (1) social interaction, (2) language as used in social communication, or (3) symbolic or imaginative play.

C. The disturbance is not better accounted for by Rett's disorder or childhood disintegrative disorder.

299.80 Pervasive Developmental Disorder, Not Otherwise Specified

This category should be used when there is a severe and pervasive impairment in the development of reciprocal social interaction or verbal and nonverbal communication skills, or when stereotyped behavior, interests, and activities are present, but the criteria are not met for a specific pervasive developmental disorder, schizophrenia, schizotypal personality disorder, or avoidant personality disorder. For example, this category includes "atypical autism" --presentations that do not meet the criteria for autistic disorder because of late age of onset, atypical symptomatology, or subthreshold symptomatology, or all of these.

299.80 Asperger's Disorder

A. Qualitative impairment in social interaction, as manifested by at least two of the following:

(1) marked impairment in the use of multiple nonverbal behaviors, such as eye-to-eye gaze, facial expression, body postures, and gestures to regulate social interaction

(2) failure to develop peer relationships appropriate to developmental level

(3) a lack of spontaneous seeking to share enjoyment, interests, or achievements with other people (e.g., by a lack of showing, bringing, or pointing out objects of interest to other people)

(4) lack of social or emotional reciprocity

B. Restricted, repetitive, and stereotyped patterns of behavior, interests, and activities, as manifested by at least one of the following:

(1) encompassing preoccupation with one or more stereotyped and restricted patterns of interest that is abnormal either in intensity or focus

(2) apparently inflexible adherence to specific, nonfunctional routines or rituals

(3) stereotyped and repetitive motor mannerisms (e.g., hand or finger flapping or twisting, or complex whole-body movements)

(4) persistent preoccupation with parts of objects

C. The disturbance causes clinically significant impairment in social, occupational, or other important areas of functioning.

D. There is no clinically significant general delay in language (e.g., single words used by age 2 years, communicative phrases used by age 3 years).

E. There is no clinically significant delay in cognitive development or in the development of age-appropriate self-help skills, adaptive behavior (other than in social interaction), and curiosity about the environment in childhood.

F. Criteria are not met for another specific pervasive developmental disorder or schizophrenia.

Embryonic Stem Cells No Magic Bullet

Evangelical Christians have been accused of being anti-science for two reasons: opposing neo-Darwinian evolution and opposing embryonic stem cell research.  While the former argument is fair, the latter is not. Science does not want to be ethically judged from the outside. How dare you place strictures about a therapy that was so self-evidently the next big thing? The Bush Administration was excoriated for only supporting stem cell lines that were corrupted by mouse cells. Scientists argued we cannot do good research based on these defective stem cell lines. Now they have a bigger problem. The stem cells mutate in the same way cancer cells do.

News @ nature.com is reporting that Gene defects plague stem-cell lines.

Embryonic stem cells that are cultured in the lab accumulate an alarming array of genetic changes, including mutations known to be linked to cancer. The finding throws into question whether such cells could eventually be used for therapy, unless they can be kept fresh and checked for mutations before use.

Researchers think that stem cells, which can be programmed to grow into any kind of cell, could one day be used to regenerate or replace cells and organs damaged by disease. But growing these cells has proven problematic.

In January, researchers announced that most human embryonic stem-cell lines, including ones approved by the US government for use in federally funded studies, have been contaminated by animal cells used as a growth medium in lab dishes. Any cell containing such foreign proteins would presumably trigger a damaging immune response if transplanted into a human patient. Researchers realized they would have to grow their cells differently in order to use them for therapy.

Now another difficulty has come to light. The longer the cells are kept, and the more they divide, the more errors they build up in their genetic code. "These mutations we are finding are a much bigger problem," says Aravinda Chakravarti of the Johns Hopkins University in Baltimore, Maryland.

How does this happen?

All DNA tends to accumulate mutations as it divides, because each step in the copying process can introduce errors. But previous, smaller studies of stem cells had not found problematic levels of mutations.

Chakravarti and his colleagues decided to take a closer look, examining nine of the human embryonic stem-cell lines that have federal approval. They compared frozen, archived cells with 'daughter' generations that had been created from these.

Many of the archived cells seemed normal, although some had already divided tens of times to build up cell numbers into the billions. But errors began to appear after further divisions. Out of nine cell lines, eight developed one or more genetic changes commonly observed in human cancers, the team reports in Nature Genetics¹.

The researchers make the following damning assessment:

The finding undermines a general assumption that stem cells remain unblemished until they are programmed to become a certain type of cell. "This is not good news. It suggests that the biological properties of the cells before and after replicating could be different," says Chakravarti.

Does this argue just against the federal lines because we need to replicate them more? That's the argument made by Roger Pedersen:

Stem-cell expert Roger Pedersen of the University of Cambridge, UK, says he takes a "glass half full" view of the findings, because the billions of archived cells seemed normal. This shows that the replications needed to boost stem-cell numbers to usable levels do not necessarily cause problems.

Pedersen adds that the study supports the idea that more, fresh stem-cell lines would be useful for the scientific community: US federal research currently relies on a very limited number of lines.

My response is that this shows a possible defect in the whole approach given the small number of stem cells in a blastocyst. Thus, you need to be replicate the stem cells and at the same time you need to minimize the number of generations from the original stem cells. The problem may not be detectable -- the billions of cells seemed normal -- until the number of generations is increased. The bottom line is that a source other than human embryos is needed for better, fresher stem cells.

Colorado State Forecasts More Bad News For Hurricanes

Link: FORECAST OF ATLANTIC HURRICANE ACTIVITY FOR SEPTEMBER AND OCTOBER 2005.

Following a record amount of June-July tropical cyclone activity and an active August in which Hurricane Katrina caused the greatest economic loss ever inflicted by a hurricane on the United States, we are continuing the bad news by predicting above-average activity for September and October. This year should be one of the most active and is already the most destructive hurricane season on record.

This cannot be good news for the hurricane-ravaged gulf coast. CSU was also right on the money for their August forecast:

Eric Blake spent from 1998-2001 as a graduate student at Colorado State University. His research efforts went into the development of an Atlantic basin August-only hurricane forecast scheme which was used for our 5 August 2005 forecast. See Blake (2002) or Blake and Gray (2004) for background information. Our August 2005 forecast called for well above-average activity, and this forecast verified remarkably well.

CSU forecast and verification of August-only hurricane activity made in early August

Tropical Cyclone Parameters and	August 2005	Adjusted August	August 2005
1950-2000 August Average (in parentheses)	Statistical Forecast	2005 Forecast	Verification
Named Storms (NS) (2.8)	3.2	5	5
Named Storm Days (NSD) (11.8)	12.1	20	21
Hurricanes (H) (1.6)	1.3	3	2
Hurricane Days (HD) (5.7)	6.7	10	7
Intense Hurricanes (IH) (0.6)	0.9	1	1
Intense Hurricane Days (IHD) (1.2)	2.8	3	2.5
Net Tropical Cyclone Activity (NTC) (26.4)	33.7	50	42

The CSU hurricane experts do not believe that global warming has anything to do with additional hurricanes.

Many individuals have queried whether the unprecedented landfall of four destructive hurricanes in a seven-week period during August-September 2004 and the landfall of two more major hurricanes in the early part of the 2005 season is related in any way to human-induced climate changes. There is no evidence that this is the case. If global warming were the cause of the increase in United States hurricane landfalls in 2004 and 2005 and the overall increase in Atlantic basin major hurricane activity of the past eleven years (1995-2005), one would expect to see an increase in tropical cyclone activity in the other storm basins as well (ie., West Pacific, East Pacific, Indian Ocean, etc.). This has not occurred. When tropical cyclones worldwide are summed, there has actually been a slight decrease since 1995. In addition, it has been well-documented that the measured global warming during the 25-year period of 1970-1994 was accompanied by a downturn in Atlantic basin major hurricane activity over what was experienced during the 1930s through the 1960s.

We attribute the heightened Atlantic major hurricane activity between 1995-2005 to be a consequence of the multidecadal fluctuations in the Atlantic Ocean thermohaline circulation (THC) as we have been discussing in our Atlantic basin seasonal hurricane forecasts for several years. Major hurricane activity in the Atlantic has been shown to undergo marked multidecadal fluctuations that are directly related to North Atlantic sea surface temperature anomalies. When the Atlantic Ocean thermohaline circulation is running strong, the central Atlantic equatorial trough (ITCZ) becomes stronger. The stronger the Atlantic equatorial trough becomes, the more favorable are conditions for the development of major hurricanes in the central Atlantic. Since 1995, the THC has been flowing more strongly, and there has been a concomitant increase in major hurricanes in the tropical Atlantic.

Dr. Gray gave an explanation in English :-) for National Geographic. Note thermohaline circulation above is a more technical description of why salt content affects sea surface temperature which is a main driver for hurricane intensity. One should note that global warming would melt the polar ice caps, decreasing the salinity, reducing sea surface temperature,  and thus potentially decreasing the intensity of hurricanes.

CSU's Gray and Klotzbach say the stormier summers are part of a well-established cycle of fluctuating hurricane activity. The cycles are caused by ocean currents that alter the salt content of the water, Klotzbach said. When the salt content is higher in the Atlantic—as it is now—the water is warmer, and that causes more tropical storms to form.

When the salt content is lower, the water is cooler and fewer hurricanes form, Klotzbach said.

The cycles take 25 to 40 years to run their courses. The present cycle of increased hurricanes started in 1995 and is expected to continue for at least another decade, perhaps longer.

Klotzbach said that if global warming were affecting hurricane formation, more storms would be forming around the world instead of only in the Atlantic Basin, which includes the Atlantic Ocean, the Caribbean Sea, and the Gulf of Mexico.

"I really can't pick out a trend of increased hurricanes around the world," Klotzbach said. "If you look at the eastern Pacific Ocean, hurricane activity there has gone way down since 1995. There's no trend toward more storms there. It's a tricky problem."

 

Walk For Autism

The National Alliance for Autism Research (NAAR) is getting ready for its annual signature event, Walk F.A.R. for NAAR, which is a Walk for Autism Research. Because we have an autistic son,  our family is planning to be a part of that Walk in Denver and I am asking you to join me in raising critically-needed funds for autism research by making a contribution in support of our Walk.

Autism is a complex brain disorder that often inhibits a person's ability to communicate, respond to surroundings, or form relationships with others. First identified more than 50 years ago, autism is typically diagnosed by the age of two or three. Autism affects people of all racial, ethnic and socioeconomic backgrounds.

Few disorders are as devastating to a child and his or her family. While some people with autism are mildly affected, most people with the condition will require lifelong supervision and care and have significant language impairments. Many children with autism will never be able to tell their parents they love them.

Currently, the causes of autism are unknown and there are no specific medical treatments or cure. Physicians have no blood test or scan that can definitively diagnose the disorder. As such, the diagnosis of autism is based solely upon observations of behavior. Despite increasing national interest and high prevalence, autism research is one of the lowest funded areas of medical research by both public and private sources.

Whatever you can give will help! I greatly appreciate your support whether financially or through your prayers.

Shuttle Undone By Environmental Regulation

It has been alleged that environmental regulations have undone the Space Shuttle. That's because a freon-based foam adheres better to the tank than a non-freon-based one.

Environmental requirements requiring removal of freon from the process for spraying the foam insulation onto the tank. NASA has said that the freon-free application method resulted in foam that initially did not adhere to the tank as well, but changes were later made to strengthen the bond of the environmentally friendly foam.

Let's see if this is true. First, a diagram from the Columbia investigation of the various insulation types.

Now a diagram from NASA showing where the failure occurred on Discovery. More detailed pictures to be found at California Yankee.

The foam that failed is NCFI 24-124. Again from the Columbia report.

Most of the External Tank is insulated with three types of spray-on foam. NCFI 24-124, a polyisocyanurate foam applied with blowing agent HCFC 141b hydrochlorofluorocarbon, is used on most areas of the liquid oxygen and liquid hydrogen tanks. NCFI 24-57, another polyisocyanurate foam applied with blowing agent HCFC 141b hydrochlorofluorocarbon, is used on the lower liquid hydrogen tank dome. BX-250, a polyurethane foam applied with CFC-11 chlorofluorocarbon, was used on domes, ramps, and areas where the foam is applied by hand. The foam types changed on External Tanks built after External Tank 93, which was used on STS-107, but these changes are beyond the scope of this section.

So, what's BX-250 and HCFC 141b? Let's ask NASA.

Environmental Protection Agency

In 1987, the United States and 45 other nations adopted the "Montreal Protocol on Substances that Deplete the Ozone Layer." Under the Protocol, class I ozone depleting compounds, such as chlorofluorocarbon 11 known as CFC 11 -- the Freon-based blowing agent used in the production of the External Tank's foam -- was to be phased out of production by the end of 1995. Production of these compounds after 1995 is allowed only by "Essential Use Exemption" and must have Montreal Protocol approval.

After extensive testing the External Tank project proposed hydro chlorofluorocarbon HCFC 141b as the CFC 11 replacement. HCFC 141b is a blowing agent more environmental regulation compliant. At the same time, the Environmental Protection Agency allowed the External Tank program to continue use of stockpiled supplies of CFC 11until HCFC 141b was certified for use on the Space Shuttle and phased in.

However, in 1999, the EPA proposed to expand its regulations by implementing a ban on nonessential products that release class I ozone-depleting substances under section 610 of the Clean Air Act. Under the proposed rule, sale and distribution of BX 250, used to insulate part of the External Tank, would have been banned because it contains CFC 11. NASA asked the EPA to revise the proposed rule to provide an exemption for BX 250 and other foam containing CFC 11 used in applications associated with space vehicles.

The EPA allowed the exemption but limited it to the Thermal Protection System of the Shuttle's External Tank and only allowed the use of CFC 11 as a blowing agent when no other chlorofluorocarbons are used in the foam product.

The "new" foam containing HCFC 141b was first used on the liquid hydrogen tank aft dome of ET-82 and flew on STS-79 in 1996. The foam was implemented on the tank's acreage, or its larger portions, beginning with ET-88, which flew on STS-86 in 1997. In December 2001, BX-265, which contains HCFC 141b, first flew as a replacement of BX-250. However BX250 continued to be flown as BX-265 was implemented step wise through the manufacturing process.

So, the freon-based BX-250 has replaced by the non-freon-based HCFC 141b. Is NASA passing the buck or did the EPA actually do what they said? NASA's summary is accurate, here's the EPA report.

EPA received a comment from the National Aeronautics and Space Administration (NASA) regarding the use of specific plastic foam products for the space shuttle. NASA identified one particular product, BX-250, a foam which is part of the thermal protection system of the Space Shuttle External Tank and which uses CFC-11 as a blowing agent. NASA stated that ``although extensive efforts have been made and continue to be made to replace this material, no viable alternative has been identified.'' NASA requested that EPA revise the proposed rule to provide an exemption for CFC-blown foam products in applications that are associated with space vehicles. NASA suggested that EPA consider using the same language that EPA has previously adopted under 40 CFR part 63, subpart GG (40 CFR 63.742) for the National Emissions Standards for Hazardous Air Pollutants (NESHAPs) program. NASA provided EPA with additional information concerning its proactive pursuit of potential alternative blowing agents.

Since human space flight safety is of paramount importance to NASA, prior to implementing any new material, that material must undergo a rigorous development and qualification program for which no suitable substitute has yet been identified. NASA requested that EPA consider using the language at 40 CFR 63.742:

Space vehicle means a man-made device, either manned or unmanned, designed for operation beyond earth's atmosphere. This definition includes integral equipment such as models, mock-ups, prototypes, molds, jigs, tooling, hardware jackets, and test coupons. Also included is auxiliary equipment associated with test, transport, and storage, which through contamination can compromise the space vehicle performance.

[[Page 57518]]

EPA agrees that an exception is necessary, but EPA disagrees with NASA's proposed language. This language is far broader than what EPA concludes is actually necessary based on an evaluation of the information NASA presented. If EPA were to simply exempt all foams used for any applications associated with space vehicles EPA could be exempting products where there are already suitable substitutes. NASA only provided information concerning one particular type of foam used in applications associated with the Space Shuttle External Tank.

Therefore, based on that information, through this action, EPA will modify Sec. 82.66(c) to provide an exemption for foam products manufactured with or containing Class I substances that are used as part of the thermal protection system of external tanks for space vehicles and will add the definition of space vehicles found at Sec. 63.742 to Sec. 82.62. The exemption will be limited to the use of CFC-11 as a blowing agent and where no other CFCs are contained in the foam product. Although EPA did not propose this exemption or the additional definition, they are logical outgrowths of the comment submitted by NASA and thus it is appropriate to proceed to final action without providing any additional proposal or opportunity for further comment.

Thanks EPA for killing our astronauts.

Rush Flunks Science Again

Every time Rush Limbaugh speaks about science I get nervous. Rush did it again today. He was talking about the chemical contamination caused by arctic seabirds. Rush didn't read the story linked above very carefully because he was thinking that the contamination was natural and the bird droppings did not contain any man-made compounds. The abstract of the study in Science betrays this point:

Long-range atmospheric transport of pollutants is generally assumed to be the main vector for arctic contamination, because local pollution sources are rare. We show that arctic seabirds, which occupy high trophic levels in marine food webs, are the dominant vectors for the transport of marine-derived contaminants to coastal ponds. The sediments of ponds most affected by seabirds had 60 times higher DDT, 25 times higher mercury, and 10 times higher hexachlorobenzene concentrations than nearby control sites. Bird guano greatly stimulates biological productivity in these extreme environments but also serves as a major source of industrial and agricultural pollutants in these remote ecosystems. [emphasis mine]

DDT, Hg, and HCB are not naturally occurring compounds. The study makes the exact opposite point that Limbaugh does. In addition to atmospheric drift, seabirds are vectors that contaminate the Arctic even though it is far away from the original source of the contamination.

Evolutionary Straw Men

The New York Times reported today that a leading theologian of the Roman Catholic Church is concerned that the view of the Church with respect to evolution is being misrepresented.

The cardinal, Christoph Schoenborn, archbishop of Vienna, a theologian who is close to Pope Benedict XVI, staked out his position in an Op-Ed article in The New York Times on Thursday, writing, "Evolution in the sense of common ancestry might be true, but evolution in the neo-Darwinian sense - an unguided, unplanned process of random variation and natural selection - is not."

He said that he had been "angry" for years about writers and theologians, many Catholics, who he said had "misrepresented" the church's position as endorsing the idea of evolution as a random process. [emphasis mine]

Evangelical and Catholic scientists expressed dismay with the Cardinal's statements.

Dr. Francis Collins, who headed the official American effort to decipher the human genome, and who describes himself as a Christian, though not a Catholic, said Cardinal Schönborn's essay looked like "a step in the wrong direction" and said he feared that it "may represent some backpedaling from what scientifically is a very compelling conclusion, especially now that we have the ability to study DNA."

"There is a deep and growing chasm between the scientific and the spiritual world views," he went on. "To the extent that the cardinal's essay makes believing scientists less and less comfortable inhabiting the middle ground, it is unfortunate. It makes me uneasy."

"Unguided," "unplanned," "random" and "natural" are all adjectives that biologists might apply to the process of evolution, said Dr. Kenneth R. Miller, a professor of biology at Brown and a Catholic. But even so, he said, evolution "can fall within God's providential plan." He added: "Science cannot rule it out. Science cannot speak on this."

So have evolutionists misrepresented the Catholic Church's doctrine or is it the other way around? The following is a description of it at the National Center for Science Education web site:

Evolutionary Creationism (EC). Despite its name, evolutionary creationism is actually a type of evolution. Here, God the Creator uses evolution to bring about the universe according to his plan. From a scientific point of view, evolutionary creationism is hardly distinguishable from Theistic evolution, which follows it on the continuum. The differences between EC and Theistic evolution lie not in science, but in theology, with EC being held by more conservative (evangelical) Christians (D. Lamoreaux, p.c). I will therefore move on to theistic evolution.

Theistic Evolution (TE). Theistic Evolution is a theological view in which God creates through the laws of nature. Not just the physical laws, either: it is acceptable to TEs that one species can give rise to another; they accept descent with modification. TEs vary in whether and how much God is allowed to intervene — some slide pretty close to Deists. Other TEs see God as intervening at critical intervals during the history of life (especially in the origin of humans), and they in turn slide closer to PCs. In one form or another, TE is the view of creation taught at the majority of mainline Protestant seminaries, and it is the official position of the Catholic church. In 1996, Pope John Paul II reiterated the Catholic TE position, in which God created, evolution happened, humans may indeed be descended from more primitive forms, but the Hand of God was required for the production of the human soul. (John Paul II, 1996).

I included the description of evolutionary creationism (my position) because I find that the description was a fair description of what I believe. The description of the Catholic view in no way described it as endorsing "an unguided, unplanned process of random variation and natural selection". I share Drs. Collins' and Miller's concerns in that the statement could drive Evangelical and Catholic scientists away from their respective faiths by removing the middle ground.

Deep Impact: Gone in a Flash

This image shows the initial ejecta that resulted when NASA's Deep Impact probe collided with comet Tempel 1 at 10:52 p.m. Pacific time, July 3 (1:52 a.m. Eastern time, July 4). It was taken by the spacecraft's high-resolution camera 13 seconds after impact. The image has been digitally processed to better show the comet's nucleus.

Image Credit:

NASA/JPL-Caltech/UMD

Here's the before picture of Comet Tempel 1 six minutes before it ran over NASA's Deep Impact probe at 10:52 a.m. Pacific time, July 3 (1:52 a.m. Eastern time, July 4). The picture was taken by the probe's impactor targeting sensor.

Image Credit: NASA/JPL-Caltech/UMD

Here's the before picture of the impactor spacecraft while it was being built at Ball Aerospace & Technologies Corporation, Boulder, Colo:

Image Credit: NASA/JPL/Ball Aerospace & Technologies Corporation

Images from other observatories follow beneath the fold.

The Faulkes Telescope North can clearly see the expanding ejecta in the coma. Attached is an image obtained by dividing an R-band image obtained at 08:35 UT by one at 06:24 UT. Positive (bright) pixels show the enhancement in R-band brightness in the inner coma at 08:35 UT. Image size is 85x62 arcsec, the apparent enhancement has a maximum brightness 2.5 arcsec from the center of the comet.

Image Credit: A. Fitzimmons and the Maui Deep Impact Workshop students and educators.

This is a series of images taken at the CFHT (Canada France Hawaii Telescope) equiped with the Megacam camera, pre- and post-impact. The images are 10s exposure time and were taken through the r filter. North is up, East is left. The field of view is about 120 x 120 arcsec, which corresponds to about 15,000 km at the comet. The three images of the animations were taken respectively at 05:50:47 UT, 05:52:59 UT, 05:54:03 UT (one pre-impact and two post impact). The increase of brightness after impact (which occurred at 05:52:24 UT as seen from Earth) is obvious on the second and third images.

Image Credit: R. Cabanac (CFHT), J. Pittichova, Y. Fernandez, K. Meech (Institute for Astronomy, Hawaii), M.B. Laychak and P. Martin (CFHT)

What Are the Limits of Conventional Computing?

For their 125th anniversary Science magazine asked the Top 25 science questions, one of which is in my area of expertise. That question is:  What Are the Limits of Conventional Computing?.

At first glance, the ultimate limit of computation seems to be an engineering issue. How much energy can you put in a chip without melting it? How fast can you flip a bit in your silicon memory? How big can you make your computer and still fit it in a room? These questions don't seem terribly profound.

Unless of course, you've actually been involved like I have in semiconductor design. It always amazes us that any of this stuff works. With time, the physics gets nastier and nastier. When I started my career we were designing 4 micron gates (the distance measured here are the length of the gate of the transistor). Now we are working on 90 nm gates and next year it will be 65 nm. We now have to worry about capacitance, resistance, inductance, setup times, hold times, on chip variation, power consumption, crosstalk avoidance, electromigration, latch up, charge antennas, planarization, leakage, and electrostatic discharge (and these are just the ones I can think of off the top of my head).

In fact, computation is more abstract and fundamental than figuring out the best way to build a computer. This realization came in the mid-1930s, when Princeton mathematicians Alonzo Church and Alan Turing showed--roughly speaking--that any calculation involving bits and bytes can be done on an idealized computer known as a Turing machine. By showing that all classical computers are essentially alike, this discovery enabled scientists and mathematicians to ask fundamental questions about computation without getting bogged down in the minutiae of computer architecture.

This is true. In fact, the basic architecture of a computer has not fundamentally changed since Turing described binary digits, von Neumann developed automata theory, and Shannon developed information theory before and during World War II.

For example, theorists can now classify computational problems into broad categories. P problems are those, broadly speaking, that can be solved quickly, such as alphabetizing a list of names. NP problems are much tougher to solve but relatively easy to check once you've reached an answer. An example is the traveling salesman problem, finding the shortest possible route through a series of locations. All known algorithms for getting an answer take lots of computing power, and even relatively small versions might be out of reach of any classical computer.

Mathematicians have shown that if you could come up with a quick and easy shortcut to solving any one of the hardest type of NP problems, you'd be able to crack them all. In effect, the NP problems would turn into P problems. But it's uncertain whether such a shortcut exists--whether P = NP. Scientists think not, but proving this is one of the great unanswered questions in mathematics.

First some definitions. P stands for polynomial time and NP stands for non-deterministic polynomial time. It is really, really important to find an order P solution. Given a fast enough traditional computer, this can be solved in reasonable time. An NP complete problem is in essence unsolvable for a computer. To see how many problems are probably NP complete check out this non-exhaustive list. If a mathematician can show P equals NP or P does not equal NP, it will be an instant Fields Medal for such an individual.

If it is the latter we may need to abandon the von Neumann architecture that has served us so well. But, how would we do that?

But there is a realm beyond the classical computer: the quantum. The probabilistic nature of quantum theory allows atoms and other quantum objects to store information that's not restricted to only the binary 0 or 1 of information theory, but can also be 0 and 1 at the same time. Physicists around the world are building rudimentary quantum computers that exploit this and other quantum effects to do things that are provably impossible for ordinary computers, such as finding a target record in a database with too few queries. But scientists are still trying to figure out what quantum-mechanical properties make quantum computers so powerful and to engineer quantum computers big enough to do something useful.

By learning the strange logic of the quantum world and using it to do computing, scientists are delving deep into the laws of the subatomic world. Perhaps something as seemingly mundane as the quest for computing power might lead to a newfound understanding of the quantum realm.

The reason why quantum computing could be so powerful is the difference between a bit and a qubit. A qubit consists of multiple entangled quantum states. A bit can be 0 or 1. A qubit consists of superpositions of whole binary strings.  Thus we can do things in parallel which we are currently doing serially. One of the current challenges is maintaining what is know as coherence. Coherence can be lost by observing the state of a qubit as a result of the Heisenberg Uncertainty Principle.

The first half of my career has been marked by doing the same thing but making it smaller and smaller, and faster and faster. We've ridden Moore's Law far longer than I had personally anticipated. The question for the second half of my career is whether we will see Python's (Monty) Law: "And now for something completely different."

Pathological Science

Since I am in both the scientific and Evangelical communities, I've used my position to explain the scientific community to the Evangelical one, specifically the subgroup that believes in YEC and ID. Now I'm going to turn it around. When the scientific community looks at things like YEC and ID they scratch their heads. Worse, they come up with a theocratic conspiracy theory (not very parsimonious IMHO).

Irving Landmuir gave a talk in 1953 about what he termed as pathological science. This seems to explain some of the crazy scientific conclusions. Hat Tip: Dr. Randy Isaac, Executive Director of the American Scientific Affliation. His final note is well taken "No religious group has a monopoly on pathological science."

The characteristics of this Davis-Barnes experiment and the N-rays and the mitogenetic rays, they have things in common. These are cases where there is no dishonesty involved but where people are tricked into false results by a lack of understanding about what human beings can do to themselves in the way of being led astray by subjective effects, wishful thinking or threshold interactions. These are examples of pathological science. These are things that attracted a great deal of attention. Usually hundreds of papers have been published upon them. Sometimes they have lasted for fifteen or twenty years and then they gradually die away. [emphasis mine]

Now, the characteristic rules are these

Symptoms of Pathological Science:

1. The maximum effect that is observed is produced by a causative agent of barely detectable intensity, and the magnitude of the effect is substantially independent of the intensity of the cause.
2. The effect is of a magnitude that remains close to the limit of detectability; or, many measurements are necessary because of the very low statistical significance of the results.
3. Claims of great accuracy.
4. Fantastic theories contrary to experience.
5. Criticisms are met by ad hoc excuses thought up on the spur of the moment.
6. Ratio of supporters to critics rises up to somewhere near 50% and then falls gradually to oblivion.

A lot of the "science" in ID and YEC have the above characteristics. Two approaches have come out of the scientific community in how to deal with what they believe is bad science (correctly IMHO). One treats the mistake as sincere and the other seeks to do battle with conspiracies. How the scientific community dealt with the Kansas situation is an example of the former. I encourage my scientific and engineering colleagues to continue along that path. If the other path is taken and you falsely accuse people of a conspiracy or belittle their faith it will only harden the bad science.

Intelligent Design: An Evangelical Critique

Recently, I have been very critical of Intelligent Design. Why would an Evangelical Christian, even a scientific one, do that? Am I like Phillip Johnson contends, worse than an atheist? I do this because in addition to believing that Intelligent Design is scientifically unsound, I believe that it is unbiblical. For those of you who don't care about whether Intelligent Design is biblical then this is not for you. Go to Panda's Thumb. There's plenty of fodder there. I'm speaking to those who do care.

There are numerous passages of Scripture that deals with God as designer. One of them is Psalm 139.

139:14 I will give you thanks because your deeds are awesome and amazing.²²You knew me thoroughly;²³

139:15 my bones were not hidden from you,when²⁴ I was made in secret and sewed together in the depths of the earth.²⁵

Before I get to my main point, I would like to address an issue with interpretation of Genesis in light of YEC. Note that I am using the Net Bible translation. I'm using this one because it has a good technical commentary and also has good conservative credentials (being endorsed by Chuck Swindoll and Wayne Grudem). I would like to point out note 25.

²⁵ sn The phrase depths of the earth may be metaphorical (euphemistic) or it may reflect a prescientific belief about the origins of the embryo deep beneath the earth's surface (see H. W. Wolff, Anthropology of the Old Testament, 96-97). Job 1:21 also closely associates the mother's womb with the earth.

When the science is truly uncontroverted (embryos do not grow in the ground) the possibility of metaphor and pre-scientific accommodation is allowed, even in Evangelical exegesis.  Note that kind of phraseology is used in both Genesis 1:24 where animals were produced by the earth and Genesis 2:19 where Adam is formed out of the ground. Thus, the YEC interpretation of Genesis 1 and 2 is not a necessary one. In order to show a non-literal interpretation to be the correct one (or more to the point which non-literal interpretation is correct) requires more support. My limited point here is that such an interpretation is possible.

Back to my main point. Regardless of the use of metaphor or pre-scientific accommodation, Psalm 139 is clear that the development of the embryo is designed by God. Neo-Darwinism makes the argument that embryonic development and evolution are driven by the same underlying genetic and epigenetic mechanisms. Jonathan Wells got his PhD in developmental biology. He told his colleagues at Berkeley:

Introduction to Jonathan Wells
To: Participants in the Evolutionary Biology Virtual Discussion Group
From: Jonathan Wells

Thank you for inviting me to participate in your discussions. Let me begin by introducing myself.

I first became interested in evolution as an undergraduate at Princeton, where I studied geology. Years later, I also became interested in religion and studied theology at Yale, where I wrote a Ph.D. dissertation on the 19th-century Darwinian controversies. [1] At that time, I learned that the historical conflict between Christian theology and Darwinian evolution had almost nothing to do with biblical chronology, but turned primarily on the issue of design. Pursuing my interest in evolution, I came to Berkeley in 1989 to study embryology, since understanding how organisms develop is obviously relevant to understanding how they evolve. I am now finishing a second Ph.D. dissertation on mechanisms of early development in frog embryos. [emphasis mine]

Back then Jonathan Wells saw a connection. Now he participates in seminars that says there is a discontinuity of development and evolution. Not only does he seek to go against evolution but also against development. Note this quote:

To be sure, genes (DNA sequences) affect development, but many lines of research suggest that body plans and other morphological features are laid down prior to and largely independently of gene expression.

Excuse me? How come identical twins are identical? Identical genes by and large produce identical morphology. In his nonsensical mess, he does give a decent definition (if you take out the allegedly and note that natural selection is not the only mechanism for genetic change):

In neo-Darwinism, evolution is explained by the natural selection of small mutational changes in the "genetic programs" that allegedly control embryonic development.

Why am I making such a big deal about the connection between development and evolution?  Biblically speaking, development is designed. If something else uses the same or similar mechanism as something already shown to be designed then you have an effective argument that the evolutionary process is designed also.

There is one very big practical problem with my argument, though. It is not a scientific argument, but it's a Biblical one. The apologetic value is slight because it argues for evolution to Evangelicals but doesn't argue the Gospel to evolutionists. This should not be sneezed at however because there are many young Evangelical scientists who might not now lose their faith because they are persuaded that the evolutionary mechanism is true.

There is a reason why science cannot answer this question. ID needs to understand a theological concept known as concursus. Concursus is the doctrine that God in his Providence acts through and with second causes.  (Second causes are those things in which God acts indirectly.)  God's design while not hidden from His children is thus hidden from science. Trying to prove design from science is a fool's errand. Or put differently, if you want to know if something is designed, talk to the designer.

Not So Privileged Planet

Just as Privileged Planet  premieres June 23 at the Smithsonian comes this discovery of a rocky exoplanet as reported by news @ nature.com:

The hunt for worlds outside our Solar System has found its smallest planet yet: it weighs in at just seven-and-a-half times the size of the Earth.

Astronomers have already found more than 150 extrasolar planets, also known as exoplanets. But all of them are larger than Uranus, which has 15 times Earth's mass. The recent find is so small that it is likely to be rocky, its discoverers say, rather than a gas giant.

"This is the smallest extrasolar planet yet detected," says team member Paul Butler of the Carnegie Institution in Washington DC. "It's like Earth's bigger cousin."

Is there more to come? Probably.

"The fact that you have a rocky planet inside two gas giants makes it look a lot like our own Solar System," agrees Alan Boss, an astronomer at the Carnegie Institution who was not involved in the research.

Boss adds that the prospects of finding similar planetary systems are good, because stars like Gliese 876 are extremely common. "They're all over the place," he says, adding that of the 400 or so stars within 33 light years of Earth, about 300 of them are in the same class as Gliese 876

The team now hopes to find rocky planets around other red dwarfs in our Galaxy.

Artwork Credit: Trent Schindler/NSF

Stone Cold Mars

Last year, I reported about a possibility of microbes on Mars because of a large amount of methane. Another possibility has come up -- dare I say more parsimonious?

In today's Nature:

When methane was found in Mars's atmosphere last year, the media (and many scientists) seized on the idea that it was a whiff of life from martian bacteria. As estimates of the gas grew, so did column inches on the hopes of finding microbes.

But the real source may be far more mundane: chemistry. Geologists have calculated that given a supply of water and carbonates, just 80,000 tonnes of the mineral olivine would be enough to generate a year's worth of methane. Another paper reports a Cuba-sized olivine field on Mars's surface, and suggests there may be more beneath. Could the prospects for life be stone dead?

A Sample of One

AIDS researchers in New York apparently cried wolf. The Los Angeles Times reported:

The announcement from New York health officials in early February was chilling: A single patient had progressed from HIV infection to AIDS in months rather than years, and his strain of the HIV virus seemed impervious to normally effective medicines.

The patient, a gay man in his 40s, had unprotected anal intercourse with scores of partners. Headlines of a potential new killer spread around the world.

"This case is a wake-up call," Dr. Thomas R. Frieden, New York City's health commissioner, said at a news conference where he issued a warning for physicians to prepare for a possible new phase in the epidemic.

Yet several AIDS experts immediately questioned the importance of the case and the strategy of publicizing it so widely.

Months later, those doubts seem to have been confirmed.

No super-strain has emerged. The patient, whose name has been withheld, has responded to drug therapy. No one — not even the man's known sexual partners — was found to be infected with the same HIV strain.

The problem was there was only one patient that sparked the panic. The LA Times continues:

Some AIDS specialists now say the New York announcement was scientifically naive and needlessly alarmist — risking the effectiveness of future prevention efforts.

"Does it do good to [mislead] people and exaggerate?" asked Dr. Robert Gallo, co-discoverer of the virus that causes AIDS. He condemned Frieden's far-reaching conclusions as "scientifically, completely invalid, without a shred of evidence."

Dr. Gallo has an excellent point. Using a sample of one is not scientifically valid. Given the danger of a super-strain of AIDS I understand why the researchers dropped the ball. Nevertheless, this story is a cautionary tale about having too small a sample set.

Earlier on the Blinne Blog I commented on the politics of the movie, Privileged Planet, but I refrained from commenting on the content of the speculation. (I call it a speculation rather than a hypothesis because I don't know how this is falsifiable.) Like the AIDS researchers, much of the idea of a rare earth depends on a sample size of one. How do we know that life needs Carbon or water? Given extremophiles (life that lives in extreme environments, e.g. ingests arsenic, lives at extreme temperatures or without oxygen) how do we know that Earth is in a Goldilocks-style sweet spot? The answer is we don't because we have a sample of one. We can give all the probabilities in the world but they mean nothing if they are plus or minus 100%.

Is life unique on Earth? We don't know and the only way we will know if we find life somewhere else and thus prove life is not unique. SETI has the same problem as the Privileged Planet. The fact that E.T. hasn't phoned home means absolutely nothing. One of the motivations for Privileged Planet was to refute Carl Sagan's notion of our planet's mediocrity. Carl Sagan was in love with SETI. It's somewhat ironic that both fell into the same pit.

Christian Apologist Lead Astray By Intelligent Design Movement

Update: A reader notified me that the way I quoted was unclear. I've reformatted my entry to make it clear who is talking.

As you will see from the following interview Lee Strobel has a subtle, penetrating, mind and this has served him well in his apologetics works. But, he's not a scientist and he is dependent on scientists who are Christians to give him good information. Unfortunately, he has not been served well by them. Hat Tip: Short Attention Span.

Strobel is interviewed by  Christianity Today Magazine.

Christianity Today: You start your book with a scene with you as a young reporter. You're sent to West Virginia, where a bunch of religious townspeople are protesting the teaching of evolution in their textbooks. I was wondering if you thought that some of the things going on in public schools today would be similar to that.

Lee Strobel: If you look at public opinion polls, the public at large is generally skeptical about Darwinism.  It just doesn't ring true to a lot of people. There's an underlying widespread skepticism that neo-Darwinism could explain the diversity of life.

I take a different approach to that than some people do. I want more evolution to be taught, not less. What I mean by that is, right now, students are only getting one side of the coin. They're only getting a cursory overview of what neo-Darwinism is and being told some facts that some people believe support it. I want them to hear more about it. I want them to hear the evidence that challenges neo-Darwinism. I want students to be able to critically think about whether or not this makes sense. I want them to be free to follow the evidence wherever it points. That, to me, is academic freedom, that they should be able to pursue the evidence.

I'm not saying that Intelligent Design ought to be taught in public schools. I am saying that kids ought to be open to possibilities and pursue the evidence wherever it points, including in that direction.

The Blinne Blog: Give Strobel some points for not just cheer leading for Intelligent Design. You get the sense (and this is near-universal in the Evangelical community) that if you laid all the cards on the table Intelligent Design has the winning hand. Other more subtle proponents might say Intelligent Design doesn't have a strong hand, but neo-Darwinism has a weaker one. This is the root of the average Christian's opposition to how Darwinism is taught in the Public Schools.

And it is a pack of goods.

First Young Earth Creation and now Intelligent Design have been telling Christians that Darwinism is on the run. This is simply not true. There are thousands of papers describing in detail a host of evolutionary pathways. These pathways include many of Behe's supposedly irreducibly complex systems. Many of these papers are very recent. Not only do scientists know that the mechanisms of evolution work, but there is greater understanding how it works. The latter part could be used in a design argument because the genetic mechanism is quite beautiful. (Listen to the Francis Collins keynote on the ASA web site.) Anthony Flew is now being tauted by the Intelligent Design community. He stopped being an atheist because he believed neo-Darwinism, not because he doubted it. Design and Darwinism are not by necessity mutually-exclusive categories.  Even if the Darwinists are terribly self-deceived it is an utterly wrong to characterize them with the  "on-the-run" self-perception. Unfortunately, it is the Christian lay people who have been deceived. This produces the slander of the scientists that they are just a bunch of atheistic materialists. Some are, but many are not.

Christianity Today: How can Intelligent Design get past the creationist label?

Lee Strobel: It's always the Darwinists who bring that up. I've done this on my TV show, Faith Under Fire, where we'll have a debate between someone who is convinced of Intelligent Design versus a Darwinist. The Intelligent Design person brings up scientific data and arguments based on scientific evidence to support his or her beliefs. And then it goes to the other side, and that person is immediately accused of injecting faith and injecting religion and trying to be a subterfuge to teach the Bible in schools.

Well, time out here, who's bringing up religion? I didn't hear the Intelligent Design advocate bring up religion. It's being brought up by the other side. It's an ad hominem argument that Darwinists use to throw sand in people's eyes to suggest that this is just biblical creationism in another disguise. What I'd like to see is the debate centered on the evidence and the data. Why are people so afraid of evidence that happens to point toward an affirmation of what the vast majority of people on the Earth believe in the first place?

The Blinne Blog: As a Christian who believes in intelligent design (the concept, not the movement) I say start by  stopping the slander of scientists.  The mis-appraisal of the state of science has caused a huge mutual misconception between scientists and Evangelicals. Evangelicals say they only want the science taught. If that was so, then it would be neo-Darwinism, because the science taught by Intelligent Design is utter, complete garbage. The scientists try to figure us out and only can figure that this is just re-packaged creationism, not realizing that we really think a sow's ear is a silk purse. We really believe that in a fair fight we would win. If we don't do a brutally honest self-appraisal and fast, good men like Lee Strobel will lose their hard-fought reputation and the good they have done will be tainted.

Teaching the Controversy: A Proposal

A constant refrain from intelligent design proponents is that we need to teach the controversy. On the other side we have science educators who say, no we don't. I say use the controversy to teach good science. My proposal is a result of a challenge by Henry Gee in Nature.

What we really need is a cadre of religious scientists who can both stand up for their beliefs, and realize that they don't need intelligent design to stick their faith and work together.

These brave scientists should be prepared to expose intelligent design for the nonsense it is.

Fair enough. This Evangelical scientist will attempt to fill the gap. Here is what is needed in science education:

1. Have a clear definition of both science and methodological naturalism. Science is a natural tool seeking natural answers. There may exist supernatural answers but this is beyond the ken of science. Methodological naturalism assumes there exists a natural answer to a natural problem. If such an answer does not exist you are attempting to prove a negative and thus it cannot be done in science.
   
2. Distinguish metaphysical inferences about nature from science. I believe both in evolution and a designer. I look at the order of the Universe and the beauty of how evolution elegantly searches a solution space and I see a Designer behind it. Non-religious scientists see a self-existent Universe run by Natural Law. Science cannot tell us which metaphysical inference is true. Good grief, there's a reason why Aristotle called called this discipline "above physics". Let science be science and answer the "what" question and leave the "why" question to other disciplines. If the reason why certain topics are not brought up is because of the intentional self-limitation of the scientific method, then the conflict can be resolved without  crushing  students' faiths. The way many religious people view science is a bunch of elitists looking down and judging their faith. By stressing the deliberate limitations of science here, the misconception can be diffused.
3. Acknowledge the controversy but teach the science. This is the core of my proposal. Some of Intelligent Design theory is scientifically testable. Use these to show how science advances and what characterizes good and bad science.
   
   Behe had a number of concerns about Evolution in that Irreducible Complexity was something that Evolution couldn't overcome. Since Behe originally came up with his thesis the genomic revolution in Biology occurred. Biology students need to know how much progress has been made in Evolutionary Biology in the last decade. If you listen to the ID proponents you would think it was going the other way. By not addressing the concerns it gives science students the wrong impression that ID is simply being silenced.
   
   Here's how it would work in practice. Take some of his specific concerns about the blood clotting cascade, whale transitional forms, the vertebrate immune system etc. and show how they were addressed. These are actually good case studies of how Evolutionary Biology is done in the 21st Century and how it is different from the 19th. When you are done, stress that proving IC does not prove ID and disproving IC does not disprove ID. Science cannot answer that question.
   
   Address why ID does not show up in peer-reviewed journals. Namely, it is because of bad methodology. Americans think science is "democratic" and simply don't understand how real science is done. Here the controversy can be used to teach them. Pick up an issue of Science or Nature and go to the section on methods. Explain how a peer reviewer examines and critiques the methods to make sure that they are valid. Show how a peer reviewer looks for transparency and lack of conflicts of interest in order for the experiment to be replicated by others. A good case study can be found here. In this case study Randy Isaac plays a peer reviewer for an  allegedly censored paper by John Baumgartner. Randy Isaac is Executive Director of the ASA, a group of working scientists who are also Christians.

In conclusion, I believe that reasonable science educators and reasonable Christians can get together to improve the quality of the science education in our country. The level of ignorance of science in this country is quite high and it is not limited to just Conservative Christians. The current controversy can be taken from a huge distraction to an occasion to really teach Americans how science really works and how it is not a threat to people of faith.

Clinical Trials in Need of Reform

More on the ongoing saga of suppressing negative results of drug trials. From the front page of today's  New York Times.

When the drug industry came under fire last summer for failing to disclose poor results from studies of antidepressants, major drug makers promised to provide more information about their research on new medicines. But nearly a year later, crucial facts about many clinical trials remain hidden, scientists independent of the companies say.

Within the drug industry, companies are sharply divided about how much information to reveal, both about new studies and completed studies for drugs already being sold. The split is unusual in the industry, where companies generally take similar stands on regulatory issues.

Eli Lilly and some other companies have posted hundreds of trial results on the Web and pledged to disclose all results for all drugs they sell. But other drug makers, including Merck and Pfizer, release less information and are reluctant to add more, citing competitive pressures.

As a result, doctors and patients lack critical information about important drugs, academic researchers say, and the companies can hide negative trial results by refusing to publish studies, or by cherry-picking and highlighting the most favorable data from studies they do publish.

But that's not the half of it. In PlosMedicine Richard Smith, former editor of BMJ, cites other way drug companies corrupt the peer-review system for evaluating clinical trials:

Examples of Methods for Pharmaceutical Companies to Get the Results They Want from Clinical Trials

• Conduct a trial of your drug against a treatment known to be inferior.

• Trial your drugs against too low a dose of a competitor drug.

• Conduct a trial of your drug against too high a dose of a competitor drug (making your drug seem less toxic).

• Conduct trials that are too small to show differences from competitor drugs.

• Use multiple endpoints in the trial and select for publication those that give favourable results.

• Do multicentre trials and select for publication results from centres that are favourable.

• Conduct subgroup analyses and select for publication those that are favourable.

• Present results that are most likely to impress—for example, reduction in relative rather than absolute risk.

Given his twenty five years of experience what's Smith's cure?

How might we prevent journals from being an extension of the marketing arm of pharmaceutical companies in publishing trials that favour their products? Editors can review protocols, insist on trials being registered, demand that the role of sponsors be made transparent, and decline to publish trials unless researchers control the decision to publish. I doubt, however, that these steps will make much difference. Something more fundamental is needed.

Firstly, we need more public funding of trials, particularly of large head-to-head trials of all the treatments available for treating a condition. Secondly, journals should perhaps stop publishing trials. Instead, the protocols and results should be made available on regulated Web sites. Only such a radical step, I think, will stop journals from being beholden to companies. Instead of publishing trials, journals could concentrate on critically describing them.

I am no fan of bigger government but for information as critical as this we need a truly independent evaluation. If that cannot be done then at least the post-marketing safety analysis should be done and paid for by the government. Letting the pharmaceutical companies do these seems to be cheaper but in the long run the savings are not worth it. The temptation to rig the system is just too great.

 

Discovery Institute Messes Up

Earlier last week I heard rumblings about the Discovery Institute playing a movie entitled the Privileged Planet at the Smithsonian. As for the content of the movie, I am less opposed than usual since it is based on cosmological rather than anti-evolutionary arguments.  For the Discovery Institute to emphasize that kind of argument is a step in the right direction in my opinion. All that being said the quality of the movie is not what I will be discussing. If you want to peruse the arguments pro and con I point you to the ASA. Both proponents and critics of ID are members and we regularly debate the merits of the arguments. But I digress...

The issue started when pro-ID blogger Denyse O'Leary trumpeted how the Smithsonian was softening to ID because they were showing the movie. I madly searched the Smithsonian web site and did not find the event she was referring to. Then on Saturday the other shoe dropped.  The New York Times ran the story Smithsonian to Screen a Movie That Makes a Case Against Evolution. In the story, neither the Discovery Institute nor the Smithsonian advanced Ms. O'Leary's thesis. The PR person mentioned donations and special events policy. A ha! A hook to Google on. I found the policy and I will proceed to fisk it because I found something utterly astounding:

The Discovery Institute apparently made an unrestricted $16,000 donation to the Smithsonian!

Their movie was a party in celebration to said contribution. If I were them there would be some very nervous lawyers in Seattle. Let's analyze the policies! [All emphasis mine]

CONTACT INFORMATION

Please contact us by phone or e-mail to inquire about having your special event at Natural History! A Special Events Coordinator will be happy to answer your questions, check availability of dates, and suggest an appropriate contribution.

Note that this is a contribution and not a fee. This will be significant later.

Mailing address:

Office of Special Events
P.O. Box 37012
NMNH 2209, MRC 139
Washington, DC 20013-7012

Street address:

Constitution Avenue at 10th Street, NW
Washington, DC 20560-0139

Phone: 202-633-1650
Fax: 202-357-1602
   E-mail: nhevents@si.edu

Staff

Ted Anderson
Director of Special Events

Tina Karl
Assistant Director of Special Events

Gwen Neild
Special Events Coordinator

Debbie Williams
Special Events Coordinator

SPECIAL EVENTS POLICY

Corporations and organizations making an unrestricted contribution to the National Museum of Natural History

STOP THE PRESSES! The Discovery Institute is now trying to say they paid a fee for a room. But, the policy is clear that this is for a contribution and more to the point an unrestricted contribution. The Smithsonian may spend the $16,000 on anything they want including promoting evolution. Denyse is also arguing that the movie was not anti-evolution. Fine. If you want to split hairs, go ahead. The Discovery Institute may be restricting themselves but there is no such restraint on the Smithsonian.

may co-sponsor an event in celebration of their gift.

There's our co-sponsor language. The sponsorship has to do with the fact they are celebrating a gift and not endorsing the giver. More later.

Your gift helps to support the scientific and educational work of the Museum. Personal events (i.e. weddings, etc.), fund raising events, and events of a religious or partisan political nature are not permitted.

This is the one positive I see for the DI here. The Smithsonian judged the movie as not religious. I've heard from those who are in contact with the Smithsonian staff they were looking for things being overtly religious. Nevertheless, DI scores some points here. Both sides are spinning this so heavy that it is hard not to get dizzy. My advise to Denyse and other supports of ID is to focus on this, because the rest is a lost cause.

Cash bars, raffles and the display or promotion of commercial products are also prohibited.

All events at the National Museum of Natural History are co-sponsored by the Museum and must be planned in conjunction with one of the Museum's Special Events Coordinators.

This co-sponsoring is a point of controversy. Denyse viewed this as an endorsement. But, according to the NY Times article neither the Discovery Institute nor the Smithsonian claim this. Further, the Smithsonian claims (and the policy confirms) that they have to co-sponsor the events.

The Special Events Coordinator will be required to approve all event plans, including invitation text, speaking program, the use of logos, and vendors. The name of the Museum and the Smithsonian Institution may not be used on any document without prior approval by the Museum.

On Denyse's blog is her invitation to the event that has the logo of the Smithsonian on it. The fact that her invite has the Smithsonian logo on it indicates that this event was under the policy. If this was some paying for the auditorium, the Smithsonian would have disallowed the use of their logo on the invite. I am assuming that the Discovery Institute is on the up and up here because if they used the Smithsonian's logo without approval then they are truly in a world of hurt.

Caterers working within the Museum must have the required $1 million liability insurance certificate on file at the Smithsonian. Although co-sponsors may work with the caterer of their choice, the Museum reserves the right to review and approve the choice of caterer in order to assure that they are capable of working safely within the Museum and are aware of the catering limitations within the building. The Museum's special events staff can also provide a list of caterers and other vendors who have successfully handled events in the Museum.

Once an event is approved, co-sponsoring organizations will receive a confirmation letter and an agreement form  outlining the basic parameters of the event and the fees. Required fees include the tax-deductible contribution[!!] and direct costs (for overtime services which are provided by the Museum).

The Discovery Institute is claiming that they were just paying fees and there was a contract. This may be the root of the misunderstanding because there is a contract involved with the policy. I'll deal with the contractual aspects later. The whole contribution stuff is addressed again. There are both fees and an unrestricted donation and this may have confused the Discovery Institute.

The event will be confirmed when the signed agreement form and full payment are received by the Museum's Special Events Office.

Given this is all confirmed by the Smithsonian, all of the above have to have occurred.

Payment is required prior to the event. During periods of high demand, a non-refundable deposit may be required. In these instances, the deposit will be considered an advance payment on the required contribution.

For a complete copy of the Museum's special events policy, please contact us by phone or email.

DI should have done this. If I could find this out with a couple minutes of Googling their legal staff were not doing due diligence and should be fired. I say this because DI says they entered into a contract and all contracts should be approved by their legal counsel. Add to that the fact that a law professor is on staff at the Discovery Institute and the magnitude of the error becomes even more stunning.

Korean Stem Cell Study Produces More Ethical Dilemmas

Update: The researcher denies that these are fertilized eggs. Now the question becomes whether blastocysts created by somatic cell nuclear transfer (popularly known as cloning) is life or not. I am now less concerned but the fact that Dolly became a real sheep still troubles me. Reading the reactions that people have to this issue it seems I am the only one on the planet that feels better that this is cloning rather than IVF. This is still an ethical dilemma -- just not as profound as when I originally posted this.

"I think this construct is not an embryo," he said. "There is no fertilization in our process. We use nuclear transfer technology. I can say this result is not an embryo but a nuclear transfer construct." The sheep Dolly, the first adult mammal cloned, was made using nuclear transfer, in which the nucleus is removed from an egg cell, replaced with the nucleus of the animal or person to be cloned, and then fused. The egg begins dividing as if it had been fertilized and sometimes becomes an embryo.

 

A new South Korean study has announced the ability to produce immune-matched, patient-specific human embryonic stem cells (hESCs).  The good news is that would allow for less rejection. The bad news is this will increase the number of stem cell lines needed per patient. When you get into the details of the study it gets even more ominous.

There are two techniques used: injection and fusion. The mean number of injected oocytes (read human beings might be killed because these are fertilized cloned eggs [RDB note: because of the update above my conclusions are more tenative here]) per line (read patient because every patient will want a matched stem cell line) is 16.8 and 13.8 if the donor is less than 30 years old. The numbers are 11.7 and 10.0 for fusion respectively.

The difference in success rate with respect to age is important because of how the fertilized eggs would be harvested. The common characteristic of fertilized eggs coming from fertility clinics are that the mothers are usually over 30 years old. Thus, the donors of the eggs would have to come from women who donate it for that explicit purpose.

The Koreans have already have been dogged by ethical breaches.

Seoul - When, in February [2004] , a South Korean team announced that it had derived stem cells from a cloned human embryo, its achievement was heralded as an important step on the road to 'therapeutic cloning'. But the research is now clouded by nagging questions about the source of the key resource for the experiment: human egg cells.

Korean citizens'-rights activists and bioethicists are pressing the team, led by Woo Suk Hwang and Shin Yong Moon of Seoul National University, to prove that the recruitment of women volunteers followed ethical guidelines. Nature's enquiries have also revealed troubling inconsistencies — in particular over whether the donors included junior members of the research team.

The brewing controversy could undermine the domestic public and political support on which Hwang and Moon's progress has depended (see News Feature, page 12). Any suggestion of ethical irregularities in therapeutic-cloning research could also have international repercussions, providing ammunition for activists who are opposed to the technology on moral grounds.

Therapeutic cloning involves creating an embryo by transferring the nucleus from a patient's cell into a human egg cell stripped of its own nucleus. After being grown in culture for a few days, this clone can yield embryonic stem cells, which can develop into any of the body's tissues. Because these would be derived from the patient's own cells, there should be no problem with immune rejection in using grafts derived from them to repair diseased or damaged tissues.

But cloning is very inefficient. To derive a single line of embryonic stem cells, the Korean team used 242 eggs obtained from 16 volunteers (W. S. Hwang et al. Science 303, 1669–1674; 2004). Each woman was given hormone injections to force her ovaries to superovulate, producing 12–20 eggs per menstrual cycle instead of one.

Other researchers were surprised that so many women were prepared to undergo this procedure for a research project. Side effects of the treatment can range from general discomfort and emotional stress to clotting of the veins or stroke. "It's a painful procedure and there is risk involved," says Jose Cibelli, a co-author on the paper who studies cloning at Michigan State University in East Lansing. "It would never fly in the United States."

Hwang says that the donors were motivated by a desire to push forward a promising field of medicine. "Many women are sympathetic with our research," he says. Supplementary material published online with the paper says that the volunteers were not paid, and explains that they filled in informed-consent forms detailing how the eggs would be used.

Egg donations

The donors were anonymous, but one PhD student in the team, Ja Min Koo, initially told Nature that the donors included herself and another woman in the lab. She subsequently called back and said that she had not donated eggs, blaming her poor English for a misunderstanding. But in the initial interview, she named the hospital where her donation was carried out, and explained that she had been happy to donate eggs because she already has two children.

Art Caplan, who heads the Center for Bioethics at the University of Pennsylvania in Philadelphia, argues that it would be bad practice if egg donors for such a project included students or junior employees on the research team because "it could certainly look like coercion was involved".

The information posted with the paper also states: "Neither donors nor their family, relatives or associates may benefit from this research." Koo, who was a co-author on the paper, arguably did stand to gain professionally from its publication.

Hwang denies that Koo was among the donors. But he declined Nature's requests for further documentary evidence of the procedures for recruiting the egg donors and obtaining their consent. Attempts to get more information from the Institutional Review Board at Hanyang University Hospital in Seoul, which provided ethical approval, were similarly rebuffed. Its chair, university obstetrician Moon-il Park, cancelled an arranged phone interview.

Within Korea, concern is growing about the lack of transparency surrounding the procedures for obtaining the donated eggs. "I'm doubtful women would give their eggs so easily," wrote Pil Pyul Lee, a science historian at the Korea National Open University in Seoul, in the 23 February issue of the Professors Times, a nationwide newspaper in which academics express their views on topical issues.

Lee's article also questioned the inclusion as a co-author on the paper of Ky Young Park, a plant molecular biologist formerly at Sunchon National University who is now a science and technology adviser to South Korean President Roh Moo-hyun. Park says that she has played an important role in Hwang's research over the years by advising him on public attitudes to his work with transgenic livestock, but she told Nature that she had no specific involvement with the therapeutic-cloning paper.

One of South Korea's leading citizens'-rights groups, People's Solidarity for Participatory Democracy, now says that it will look into the ethical issues surrounding the cloning paper. "We plan to pressure the government to force them to produce the documents that are required," says Jae-kak Han, who heads the group's scientific division. The Korean Bioethics Association is also pressuring the National Human Rights Commission to look into the matter.

Welcome to the brave new world. Most people oppose cloning people for spare parts but this will probably slide because the spare parts are so small. But -- make no mistake -- that is precisely what is going on here. There will be a great temptation to do this for money or pressure from families of sick relatives etc. At the end of many movies there is a disclaimer that no animals are harmed while producing the movie. Even in this limited experiment, 210 human beings may have died. Even if every stem cell line literally saved a life, an order of magnitude more of lives are lost every time.  Victor Frankenstein would be proud.

Fair Play

Chuck Colson opined concerning fair play in the Kansas evolution controversy.

Americans believe in fair play. If a football or baseball team doesn’t show up, it forfeits the game. If the defense lawyer in a trial puts on no case, the judge is likely to declare a summary judgment to the plaintiff. You play by the rules, or you don’t play.

So why have so many evolutionists apparently decided that the rules don’t apply to them?

This pattern is surfacing once again in Kansas, where you may remember a huge controversy broke out a few years ago, and the evolutionists squashed any other teaching in Kansas.

 

This time the new state board of education is holding hearings to consider revisions that a group of scientists and educators has called for. These would allow Darwin’s theory of evolution to be taught in schools, but they would permit scientific challenges to Darwinism to be taught as well.

The principles espoused by Mr. Colson are good ones. Playing fair in the midst of controversy is a very good principle. Indeed, it is a Christian one. Now for the rest of the story. Keith Miller gave the following explanation for the boycott of the Kansas hearings.

A short explanation for the decision by the scientific community throughout Kansas to not participate in the hearings.

The hearings were set up completely outside of the established process for revising sc