The Alternate RNA Universe
November 29th, 2007
Most of us who research viruses have at least a passing acquaintance with the hypothesis known as “RNA World”. It posits that RNA was the first genetic material, partly because it can act as both genetic information AND enzymes to copy that information and – possibly – to make proteins and other cellular components.
Recently, I was granted a glimpse into a far stranger world, one that I have come to call the “Alternate RNA Universe”.
A few weeks ago, a well-meaning family friend sent me a link to the most amazing website (which will not be repeated here – I don’t want to give them any free advertising) that claimed to cure pretty much every chronic illness – from adrenal “deficiency” to tick-borne diseases – with RNA!
Well, this piqued my interest. I work with RNA quite a bit and I have a good deal of experience in handling RNA and using it to silence gene expression.
The first thing I did was to check the ingredients. Each half milliliter contained:
“Proprietary Blend of Nucleotides (Saccharomyces cerevisiae, cytidine-5′-monophosphate, adenosine-5′-monophosphate, guanosine-5′-monophosphate) – 5 mcg”
That’s 5 micrograms of RNA nucleotides in each half milliliter of RNA solution. The source of the RNA is listed as Saccharomyces cerevisiae, a common yeast that’s become a regular “lab rat” in molecular genetics. It’s easy to grow and contains a lot of RNA, so it would be the logical choice.
Curiously, the website also claims that their product, “Does not contain yeast, sugar, dairy, wheat, corn, soy, artificial colors or flavors.” I guess they don’t consider the ribose sugar (the “R” in RNA) to be a “real” sugar.
[Note: they've also added the standard "weasel words" - "These statements have not been evaluated by the FDA. This product is not intended to diagnose, cure or prevent disease. Always consult with your professional health care provider before changing any medication." In other words, they claim that their nostrums cure diseases, but they really aren't claiming that they cure diseases...wink, wink, nudge nudge, say no more.]
OK, so far you’ve got 24 ml of RNA solution (a “Proprietary Blend”, no less) containing a grand total of 240 micrograms of ribonucleotides. And how is this supposed to help cure you of your ills, you ask?
Beats me.
It apparently is beyond the grasp of the people who are promoting it, as well. I looked at every publication, article, op-ed and testimonial the website directed me to – including the very amusing website of Dr. Garry Gordon – and all I could find were references to RNA interference, siRNA and the like.
The only problem is that RNA interference, siRNA, and the rest all require polymerized RNA. Sure, they’re short strands, but none of it works with the monomers (nucleotides) that are in the bottle of RNA solution.
But this little problem hasn’t stopped the promoters of the Alternate RNA Universe. Let me provide you with some extracts from an article (Explore, vol. 13, no. 6, 2004) by Amy Yasko and Garry Gordon: “Heal Your Body Naturally: the Power of RNA”.
“We have found that by using highly specific solutions of RNAs we are able to enhance our cells natural ability to communicate with one another.”
This would be earth-shaking news…if it were true. The sad fact is that the cells in our body have a “thing” about stray RNA. There are enzymes – RNAse’s – that chew up RNA in order to prevent unauthorized “communication” from RNA viruses. These enzymes are in every cell and every body fluid.
There is enough RNAse in a fingerprint to degrade milligrams (1000 micrograms) of RNA in a few minutes. And it’s even worse if you try to ingest the RNA. There are high concentrations of RNAse in both saliva and pancreatic digestive enzymes, so it is highly unlikely that any RNA would survive to be absorbed.
Of course, since there are only single RNA nucleotides in these drops, the presence of RNAse is pretty much a moot point.
But let’s look past this little stumbling block and see what else Drs. Gordon and Yasko have to tell us about the Alternate RNA Universe.
“While RNA based nutrition may be a safe and natural way to supplement our bodies, we must recognize that giving RNA nutritional support without selecting what is appropriate for the particular needs of an individual will do some good and will clearly do no harm but it is like playing all the 88 keys on the piano at the same time; you will have sound but not music.
By integrating a knowledge of the strides made in molecular medicine within the context of molecular nutrition it is possible to take what nature has given us an abundance of and choose which notes to play to create a harmony that your body can respond to. Using highly specific natural RNAs allows you to play the exact music that your body needs to hear in order to be well.”
This just shows that people who don’t understand analogies shouldn’t use them.
There are four RNA nucleotides: adenosine, cytidine, guanosine and uridine. As monomers (as they are supplied in the RNA drops) they are the raw material for RNA polymerases, which make the various types of RNA used in the cell. If we don’t consume enough of the nucleotides in our diet, our cells have the ability to make all of them from “scratch”.
Feeding a person “highly specific natural RNAs” will have just about zero effect. Remember, we can make all of our own nucleotides, otherwise we would have died out as a species long ago.
Let’s continue.
“When we ingest a food such as sardines that has a high RNA content we are most likely eating all one hundred thousand to over one million different RNAs. Similarly, when we take a total RNA supplement, we are again absorbing all of the one million different RNAs in this mixture. If we think of each of these RNAs as children, all dashing to get through one doorway at the same time when the recess bell rings, you can begin to see why these total mixtures of RNA are not always effective. Or why eating sardines is just not the answer. The various children will be competing with each other to get through the door. Just as the various different RNAs will be competing to get into your cells.”
Again, bad analogies are no substitute for understanding biology.
It is hard to get RNA into a human cell. It has been done in the laboratory, usually by putting the RNA into a virus and using the virus to transport it into the cell. Cells don’t like foreign RNA – it must remind them of RNA viruses.
Besides, in our Universe, RNA ingested, inhaled or injected into the body is rapidly (and I mean very rapidly) by the ubiquitous RNAses. So, RNA isn’t lining up like children, all trying to get into the cell, laughing and squealing as they run along in their cute little jumpers. If RNA were competing to get into your cells, it would first have to get past the bouncer at the door: RNAse.
But, wait – there’s more!
“RNA has been shown to function in a variety of regulatory capacities. Most recently, work from Yale has demonstrated RNAs that function as “riboswitches” that do not require protein factors for function. (Nature, March 18, 2004). These riboswitches are used to sense compounds that are fundamental to all living systems. Riboswitches are dual function molecules that undergo conformational changes and communicate metabolite binding.
In addition to riboswitches, the past decade has seen the discovery of naturally occurring interfering RNAs and short interfering RNAs. Prior to that time regulatory roles have been described for ribozymes, antisense RNA, decoy RNA, aptamers, immunostimulatory CpG motifs and RNA-dependent-DNA methyltransferases as a means to regulate DNA methylation.”
All very true – and all involving polymerized RNA, not the monomers in the RNA drops. So, how is this relevant to the RNA solutions? Simple – IT’S NOT!
How do Drs. Yasko and Gordon explain their way around this little snag?
“In terms of how the highly specific natural RNAs that we have described work, the answer would likely be via every naturally occurring regulatory system that is utilized by RNA in the cells.”
In other words, “We have no idea how our ‘highly specific natural RNAs’ work, but we’re convinced that they do work.”
And their data showing that the “highly specific natural RNA” works?
Dr. Yasko’s website refers to a manuscript “submitted to the Annals of the New York Academy of Science in 2005” (and never, ever published, I might add) – “Role of RNA in Addressing Multifactorial Disease” – that presents a lot of unsupported assertions, some unrelated information and three “case studies”. There is no substantive information about what the RNA treatment actually consisted of, the diagnoses of the patients or, for that matter, any information about other concomitant therapies.
In this manuscript, Dr. Yasko describes – sort of – the process she uses in her “practice” :
“Unmodified RNAs chosen from a complete set of Saccharomyces cerevisiae RNA are successful in having positive effects on a wide variety of health conditions. This is true regardless of the mechanism of action by which these RNAs function, whether it is antisense or interfering RNAs, other modes of action, or whether they represent different facets of a variety of mechanisms.
The RNAs are chosen based on known published metabolic pathways for the function of interest. In addition, it has been Dr. Yasko.s observation that the less the RNA backbone deviates from the natural RNA configuration, the lower the concentration of RNA that is needed to affect regulatory processes. Consequently, the use of the described unmodified RNAs allows for significantly lower concentrations of RNA to be utilized, in the order of 1000 fold lower concentrations than are currently utilized with modified antisense RNA or DNA oligonucleotides.
The specific yeast RNAs are chosen from the Comprehensive Yeast Genome Database, MIPS Saccharomyces cerevisiae group. The MIPS Comprehensive Yeast Genome Database (CYGD) presents information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. Specific combinations of yeast RNAs are chosen based on biochemical pathways and interactions. On this basis, a number of specific unmodified Saccharomyces cerevisiae sequences have been selected from naturally occurring yeast RNA and have been utilized to help address a variety of health conditions.”
Wow!
You’ll have noticed, I imagine, that Dr. Yasko never mentions HOW she gets the “specific yeast RNAs” – which is really too bad. I’d love to have a way to get one specific RNA sequence out of the total RNA of an organism without modifying it. I suspect that there are a number of other molecular genetics researchers who feel the same way.
And Dr. Yasko manages to do this in what are essentially industrial quantities, if she is treating her patients with it.
But let’s get back to the RNA drops. These are – still! – just monomers of RNA. They aren’t the “specific yeast RNA” any more than a pile of individual Lego bricks are a castle or an Imperial Star Cruiser.
And if Dr. Yasko is giving her patients actual “specific yeast RNA” that is an intact mRNA (or siRNA or snoRNA or….), then it is rapidly (very rapidly!) broken down by the ubiquitous RNAse into monomers. The castle or race car or Star Cruiser becomes simply a pile of bricks, waiting to be made into something new.
In fact, RNA (especially the “unmodified” RNA Dr. Yasko feels is so special) is pretty unstable even in the absence of RNAse. It would break down in solution in a few days to weeks. I keep all of my research RNA in formamide solution at -80 degree C. It can last for up to a year under those conditions.
At least, that’s how it happens on this planet.
That’s why I believe that these reports are coming to us from (cue eerie “Twilight Zone” music) The Alternate RNA Universe.
Yes, I suspect that a rift in the space-time continuum has opened a window between that Universe and ours, allowing Internet-based communication to move between the two Universes.
How else can you explain how a medical doctor (Gordon) and a PhD microbiologist (and naturopath! - Yasko) could believe in what is – in our Universe – utter hogwash!
The truth is out there!
Prometheus
Filed under: Autism Science, Autism Treatments | 21 Comments »
HBOT: Under Pressure
November 16th, 2007
If you’re just now tuning in, we were discussing the newest fad treatment for autism: hyperbaric oxygen therapy (HBOT). In the last post, I showed how the increase in blood oxygen content was minimal and could easily (and cheaply) be reproduced by simply giving a bit of oxygen by mask.
So, if there is something to this “therapy” (and that’s a question not yet answered by its proponents), then it has to be the pressure, right? After all, what other difference is there between the mild (some might say homeopathic) HBOT used for autism and simply giving the children a little extra oxygen by mask (apart from the thousands of dollars difference in cost)?
Before we go any further, I think that a little review is in order:
What is HBOT?
Real HBOT (where the H stands for “hyperbaric”) involves placing the patient in a hard chamber (usually made of steel) and raising the pressure to 2 atmospheres (atm) or more. An atmosphere is - as the name might suggest - a pressure equivalent to the atmospheric pressure at sea level (on Earth). It is equivalent to 14.7 psi or about 101.3 KPa.
HBOT is a recognized treatment for conditions where the hemoglobin in the blood is unable to carry enough oxygen to meet the needs of the body. Carbon monoxide poisoning - where the hemoglobin is bound by carbon monoxide - severe anemia and a few other conditions respond nicely to HBOT.
Other conditions that have been treated - with limited success - by HBOT (real HBOT) are those where a part of the body (near the surface) is not receiving adequate blood flow due to an infection (e.g. diabetic ulcers, gas gangrene). In those cases, pure oxygen under extra pressure can sometimes get enough oxygen to the blood-starved tissues to allow healing and - it is hoped - a restoration of normal blood flow.
For all of these conditions, the pressure is brought up to the point where, with supplemental oxygen, enough oxygen is dissolved in the blood plasma to support life (see figure 1).
[Click on the thumbnail to enlarge; click the "back" button on your browser to return]
As figure 1 shows, the pressures needed to accomplish real HBOT are usually well above 4 atm and may be as high as 6 atm (the limit for most “hard chambers”). This sort of pressure is dangerous, as is administering oxygen at those pressures. It is not for the average physician and certainly not appropriate for home use.
HBOT, as promoted for autism, involves placing the child in an inflatable “soft chamber” and raising the internal pressure 0.3 atmospheres (4 psi) above the ambient (room) pressure. In some “protocols”, the child is also given additional oxygen; Dr. Rossignol’s published works suggest that he administers 24% oxygen during his HBOT “treatments”.
So, what does this additional oxygen (24% vs 21% in room air) at slightly elevated pressure work out to? It’s the equivalent - in terms of oxygen delivery - of administering 31% oxygen at room pressure.
You can buy a medical oxygen cylinder and face mask to deliver that amount of oxygen for the price of a single week of HBOT treatment, so why bother….unless there is something special about the pressure.
Why did the FDA approve the “soft chambers” if they aren’t any better than supplemental oxygen?:
This a question that comes up a lot: If HBOT for autism is unproven, then why are there so many companies making the “soft chambers”? And why can they claim that they are FDA-approved?
Well, it turns out that the FDA has approved these “soft chambers”… for treating altitude sickness. The FDA has also cautioned that “soft chambers” are not to be used with supplemental oxygen - most likely because of the fire hazard.
So, why is it that these “soft chambers” work for altitude sickness when they can’t significantly change the blood oxygen content at sea level? Let’s take a look at the charts from last post in a bit more detail.
If you look at the chart below (figure 2), you’ll see that blood oxygen content takes a fairly sharp drop at altitudes above about 3000 meters (10,000 feet). This happens because the atmospheric pressure drops to 0.67 atmospheres (9.7 psi or 695 millibars).
[Click on the thumbnail to enlarge; click the "back" button on your browser to return]
Figure 2.
At altitudes above 3000 meters (10,000 feet), an additional 0.3 atmospheres (atm) pressure can make a big difference in the amount of oxygen in the blood. People who have been to these altitudes know how important that little difference can be.
An additional 0.3 atm can make the difference between being breathless in Leadville, Colorado (3094 meters, 10,152 feet) and breathing easily at the beach (sea level). An additional 0.3 atm can make the difference between being in the “dead zone” at the top of Mt. Everest (8848 meters, 29,029 feet) and being merely winded on the slopes of Pike’s Peak.
Of course, you could get the same amount of oxygen by breathing concentrated oxygen (which is what pilots in unpressurized aircraft do), but it is easier to carry an inflatable “soft chamber” to the basecamp and take turns working the foot pump than it is to lug enough oxygen cylinders.
This is what these “soft chambers” are approved for - not treating autism, cerebral palsy or strokes.
But, back to the issue of pressure.
Pressure effects on the brain:
What do we know about the effects of pressure on the human nervous system? As is turns out, we know quite a bit. People have been subjecting themselves to elevated pressures almost since we were able to produce compressed air. In caissons, diving bells, hard-helmet dive suits and - more recently - SCUBA diving. There are over one hundred years of data on the subject.
We know that, at elevated pressures, the nitrogen in air becomes a mild general anesthetic, causing nitrogen narcosis (”rapture of the deep”). This happens at pressures above about 4 atm (3 atm above sea level pressure), and so isn’t likely to affect people in the “soft chambers”.
As pressures go up, the partial pressure of oxygen also goes up. Oxygen is essential to human life, but it also has its Dark Side. In fact, many of the “alternative” practitioners have made quite a big deal about how autism is either caused by or causes oxidative stress. The amount of “oxidative stress” increases as the partial pressure of oxygen increases, so HBOT can (and does) increase oxidative stress and , potentially, oxidative damage.
On an organismal level, the toxicity of oxygen manifests itself as lung damage - which can occur in a matter of days and at lower oxygen concentrations than is usually thought - as low as 50% - and as acute central nervous system (CNS) toxicity.
The general “rule of thumb” is that acute CNS oxygen toxicity doesn’t occur at less than 1.6 atm partial pressure of oxygen, so the “soft chambers” cannot reach this level, even breathing 100% oxygen. However, it has been reported at lower pressures with longer exposures and these have mostly been in healthy adults without pre-existing seizure disorders.
[Note: Just "published" today (16 Nov 2007) is a study by DA Rossignol et al in which they "treated" six (6) autistic children with 100% oxygen at 1.5 atm. This was done for 45 minutes and repeated forty (40) times. This comes perilously close to the maximum recommended exposure for healthy adults. I will leave it to my readers to decide if this is a wise course of action.]
Finally, at even higher pressures - which can only be attained using special breathing gas mixtures, people experience high pressure nervous syndrome. This has only been seen at pressures approaching 20 atm, which is far higher than even “hard” hyperbaric chambers can reach.
Fortunately, all of the bad effects of high pressure are seen only at pressure far above those that a “soft chamber” can reach. Even breathing 24% oxygen in these chambers is unlikely to cause anything more than a transient increase in superoxide dismutase and other enzymes in response to the increase in reactive oxygen species.
[Note: Adminstering any additional oxygen in a "soft chamber" goes against the FDA certification of these devices. A very recent study which used 100% oxygen in a "soft chamber" is alarming and raises the possibility of catastrophic outcomes.]
Unfortunately, there is no data to suggest that any of the good effects of hyperbaric treatment are likely to occur at the low pressures seen in “soft chambers”. In fact, it seems decidedly unlikely that any of the effects seen at real HBOT pressures are going to be clinically significant at “mild” (homeopathic?) HBOT pressures.
A question of compressibility:
The pressure issue really boils down to compressibility: what effect does pressure have on the cells, the tissue and the organism? The only effect pressure can have - apart from its effect on the partial pressures of gases - is to squeeze the cells.
Fluids, especially water, is often thought to be incompressible; this is not precisely true. Water is much less compressible than gases, but it does change volume under pressure (just not as much as gas). There are a few gas-filled cavities in the human body, but they are all (usually) connected to the outside, so that they can equilibrate with the external pressure. We are generally only aware of these cavities when they fail to equilibrate, such as when we’re flying in an airliner with a cold.
The bulk of our body is fluid (or solid - such as bone) and is much less compressible than gas. But not incompressible. So, there is some change in volume with changes in pressure.
Fortunately, the compressibility of cellular components has been studied, so we can get a “ballpark” estimate of at least the magnitude of the effects at different pressures, if not the specific effects themselves. However, given what is known about the effects of high pressure on the human nervous system (see above), the effects of pressure are not likely to be positive.
To determine compression, we first need to know the bulk modulus of the material. Water, which makes up the majority of our bodies, has a bulk modulus of 2.2 Gigapascals (GPa). This means that going from sea level pressure (1 atm) to 20 atm (~0.002 GPa) would cause a 0.09% change (decrease) in the volume of water.
Now, the place where the real action takes place in nerve cells (and many other cell types) is the cell membrane. The bulk modulus of the lipid bilayer membrane has been determined to be about 0.165 Gpa, so a change from sea level pressure to 20 atm would cause about a 1.2% change in membrane volume.
What about the “soft chambers”?
A 0.3 atm (~0.00003 GPa) change in pressure (typical for “soft chambers”) would cause a 0.02% change in the membrane volume. This is almost certainly below the threshold of perception, even in sensitive nerve cells. Any changes detected would more likely be due to the increase in oxygen partial pressure (which increases about 30%).
So, is there a chance that hyperbaric therapy might help autism? Perhaps, but not at the pressures attainable in the “soft chambers” used by most “alternative” autism practitioners.
If they really wanted to see the effects of pressure alone, the HBOT “researchers” could dilute the air in the “soft chamber” with an inert gas such as helium so that the partial pressures of nitrogen and oxygen remain the same as they are at sea level (or whatever the ambient pressure is). This would require (at sea level) a mix of 23% helium and 77% air. It would be a simple test (and safe - even breathing the mix at sea level pressure would not be dangerous, as it still contains 16% oxygen) and would finally put to rest any question about the need for (mildly) elevated pressure.
Unfortunately, the risks of using real hyperbaric therapy (not to mention the costs) outweigh the potential benefits (which are largely hypothetical and unproven), so a trial of real HBOT for autism is probably not in our future.
Conclusion:
Lacking a plausible mechanism by which “mild” HBOT (sometimes called mHBOT by its proponents) can help autism and lacking any controlled data, this therapy has little to recommend it apart from offering some vague hope of “treatment” or “cure”. It is important to also note that HBOT has failed to deliver in other disorders, from stroke to cerebral palsy, and there is little reason to think that autism will be any different.
Prometheus
Filed under: Autism Science, Autism Treatments, Critical Thinking | 28 Comments »
HBOT: Is it just a bunch of hot air?
November 9th, 2007
Hyperbaric Oxygen Therapy (HBOT) is arguably the hottest new fad in the “alternative” autism therapy world. Parents all over the US are stuffing their autistic children into zip-up “soft chambers” to experience this latest “cure”.
But what are they actually doing for (to) their children?
One hypothesis, expounded by a number of practitioners who administer HBOT to autistic children (and for a variety of other ailments), is that they are increasing oxygen delivery to the brain, and that this increase in oxygen delivery - even though it only lasts for the hour or so of the HBOT treatment, somehow (mysteriously) changes something about the brain (much hand waving at this point).
Without addressing how increasing the oxygen delivery to the brain for an hour or so might help with autism, let’s look at the claim for increased oxygen delivery.
Oxygen delivery to the brain depends largely on two factors: brain blood flow and blood oxygen content. The literature on cerebral blood flow response to HBOT is mixed, so that isn’t too helpful. Of note, none of the “studies” looking at HBOT in autism measured cerebral blood flow. And, it should be noted, the studies of HBOT that showed changes in cerebral blood flow were done at pressures of 4 and 5 atmospheres (atm) - about 60 psi. The typical “soft chamber” used in HBOT for autism can only go up to a pitiful 1.3 atmospheres pressure (only 4 psi above ambient air pressure).
How about blood oxygen content? Well, there is reason to believe that HBOT can increase blood oxygen content. In fact, just look at the graph below (fig.1), which shows the amount of oxygen in the blood (milliliters of oxygen per liter of blood) while breathing air at various pressures.
[Click on the thumbnail to enlarge. Use the "back" button on your browser to return]
The reason that the curve isn’t linear is because of hemoglobin. Hemoglobin carries the grand majority of the oxygen in the blood of most (if not all) mammals. We can’t live without it because not enough oxygen will dissolve in our blood plasma to keep us alive. In fact, one of the real uses of HBOT is to treat people who - for one reason or another - are having problems with their hemoglobin (e.g. carbon monoxide poisoning).
However, if you have functional hemoglobin, raising the pressure doesn’t do much to increase the blood oxygen content, not until you get beyond the pressures most (real) hyperbaric chambers can reach (most have a maximum of 6 atm).
And what about the zip-up “soft chambers” that folks are using for autism? They can’t hold more that 1.3 atm (at sea level). They are pressurized to only 4 psi above atmospheric pressure - less than the pressure inside a party balloon.
OK, so simply exposing your child to air at elevated pressures doesn’t have much impact. How about raising the oxygen concentration?
Figure 2 shows the effect of increasing the oxygen concentration at the pressure relevant to most HBOT used for autism.
Figure 2.
As you can see, the differences are minuscule - about 5% difference in blood oxygen content between breathing air at sea level and breathing 50% oxygen in a typical “soft chamber”. Now, it maybe that this is enough to reverse autism, but it doesn’t seem very likely. After all, you the same effect without the hyperbaric chamber.
Figure 3 shows what happens to blood oxygen content (at sea level pressure) breathing various concentrations of oxygen.
Figure 3.
To get to the same level as breathing air in a “soft chamber” only requires breathing 50% oxygen at sea level. To get to the same level as breathing 50% oxygen in a “soft chamber”, you only need 65% oxygen at sea level.
So, it looks as though the “benefits” of HBOT are not due to increasing the oxygen content of the blood. And the jury is still out on what HBOT does to the blood flow, although it should be noted that the studies showing any changes were done at much higher pressures.
But there isgood news: ”soft chamber” HBOT therapy is not capable of reaching pressures high enough to cause oxygen toxicity (that takes 1.6 atmospheres, even with 100% oxygen). Although, if people are concerned about “oxidative stress” in autism, adding more oxygen to the mix seems like a poor way to address that concern.
Dr. Rossignol, a key HBOT for autism promoter, has acknowledged that the increase in oxygen delivery is minimal and speculates that the effect he sees might be due to direct pressure effects. In my next post, I’ll “do the numbers” on that hypothesis.
Until then….
Prometheus
Filed under: Autism Practitioners, Autism Science, Autism Treatments | 15 Comments »
Affirm the Consequent, Deny the Antecedent, and don’t mess with the Excluded Middle.
November 5th, 2007
A lot of people think that Logic is for Debate Team nerds and people who like to torture undergraduates on warm Spring afternoons.
It is all that, and more!
When I was forced to take Dr. Sorenson’s Logic 1A course, I was expecting to be bored to near the brink of death - I expected to see the long, dark tunnel, bright light and long-dead relatives just before the bell rang for the end of each class.
I was wrong.
What I learned was not how to score geek-points in Debate, but how to be alert to people trying to fool me. Dr. Sorenson taught us using clippings from the daily newspaper, showing us how advertisers, political campaigns and even reporters and editors were using logical fallacies to sound convincing while deceiving us.
In the past, we have covered some of the more egregious fallacies (and the most common), particularly the Post hoc, ergo propter hoc (”After this, therefore because of this.”) fallacy and its close cousin, Cum hoc, ergo propter hoc (”With this, therefore because of this.”) which together are fallacies of false causation (Non causa pro causa - “Non-cause for a cause”).
The fallacies I’d like to discuss today are a bit harder to grasp, perhaps, than false causation, but they are just as ubiquitous in the world, including the world of “alternative” autism therapies.
Affirming the Consequent / Denying the Antecedent:
These two fallacies are two complementary halves that make up a lot of the nonsense spouted about autism and its so-called “treatments”.
For example, there has been a lot of talk about how certain patterns of urinary porphyrins are “diagnostic” of mercury toxicity. This is true to the extent that James Woods of the University of Washington has published in a number of articles on how mercury affects the excretion of urinary porphyrins (here, here and here). Of interest, he has also recently published an article showing that mercury from dental amalgams has no sigificant impact on neurobehavioral measures in children.
A number of people have claimed (and at least one laboratory is selling the tests) that this “pattern” of urinary porphyrin excretion is not only consistently found in mercury exposure (as Dr. Woods has convincingly shown), but that it is diagnostic of mercury exposure.
This is where the fallacy lesson comes in.
What Dr. Woods has shown (and, I believe, all that he is claiming) is that the pattern of urinary porphyrins is seen consistently in a setting of mercury exposure. This is not the same as saying that this pattern indicates mercury exposure.
Let me illustrate:
When my face gets sunburned, it turns red.
Therefore: If my face is red, it must be sunburned.
If I say that my face gets red whenever it gets sunburned (a consequence of my Northern European heritage), it does not mean that when my face is red, that it is always sunburned. I might be blushing, or hanging upside down, or exerting myself.
This is affirming the consequent. Just because “B” happens everytime “A” occurs (B = face getting red, A = sunburn) does not mean that whenever “B” (red face) happens that “A” (sunburn) has occurred.
In the case of the urinary porphyrins, the setup for the fallacy is something like this:
Mercury exposure causes a charateristic pattern of porphyrin excretion.
Therefore: If a person has the characteristic pattern of porphyrin excretion, they must be mercury toxic.
As it turns out, there are a lot of possible reasons why someone would have the “chracteristic pattern” of porphyrin excretion, including (but not limited to), other toxic metals, other toxic exposures and genetic abnormalities involving the enzymes engaged in porphyrin synthesis and metabolism.
This is not just idle speculation. One of the enzymes that is affected by mercury, causing the “characteristic pattern of porphyrin excretion” is uroporphyrinogen decarboxylase (UROD). UROD just happens to be the enzyme involved (impaired, as it turns out), in porphyria cutanea tarda, the most common of the porphyrias (see here).
The other enzyme Dr. Woods has implicated in the “characteristic pattern of porphyrin excretion” is coproporphyrinogen oxidase (CPO). This enzyme is impaired in heriditary coproporphyria (see here).
So, we have known disorders that involve impairment of the two enzymes that are responsible for producing the “characteristic pattern of porphyrin excretion”. And how does mercury cause this “characteristic pattern of porphyrin excretion”? By imparing the two enzymes mentioned above.
So, it is not just hypothetical that a genetic abnormality - a mutation - could cause the same “characteristic pattern of porphyrin excretion” as mercury.
To the best of my knowledge, Dr. Woods is not claiming that this “characteristic pattern of porphyrin excretion” can be used to diagnose “mercury poisoning” when there is no significant exposure to mercury. I suspect that others have mis-interpreted his findings to their own ends.
The “flip side” to affirming the consequent is denying the antecedent. Let me illustrate:
I only get headaches when it rains.
Therefore: If I don’t have a headache, it must not be raining
If I say that I only get headaches when it rains, that does not mean that if I don’t have a headache that it isn’t raining.
The Excluded Middle:
More properly called the false dilemma, this fallacy has been popular with politicians (”You’re either with us, or you’re against us!”) and demagogues since before recorded history. It consists of simply presenting two distinct choices and asserting that they are the only choices available.
I commonly run across this fallacy when parents claim that I am accusing them of lying when I doubt their stories (see here). What they have done is excluded the middle choices. In this particular example, the choices II am presented with are:
[1] The parents are presenting an accurate description of the events.
[2] The parents are deliberately telling a false description of the event (lying).
In fact, they have omitted at least one middle choice:
[3] The parents are telling what they believe to be the truth, which is an amalgam of their observations and their interpretations of these observations, their observations having been edited by their memory of the event, events preceding the events in question and events which have occured subsequently.
The same sort of fallacy arises in many of the testimonials that “alternative” autism therapy uses in place of data. The usual setup is something like:
“If you don’t treat your child with [fill in the blank] they will end up [a] in an institution [b] in a fate worse than death [c] in a life not worth living.”
These people have omitted the middle options of (not an exhaustive list):
[d] having a fairly normal life.
[e] having a happy and productive life.
[f] running a large multi-billion dollar software company.
[g] getting better anyway.
[h] being the best human being they can be.
[i] being happier than you are.
[j] …..
Prometheus
Filed under: Autism Science, Critical Thinking | 13 Comments »