Thursday, November 6, 2014

First Column in Skeptical Briefs

Trying to publish the interviews I had done in magazines of scientific disclosure, Benjamin Radford invited me to be a regular columnist of Skeptical Briefs newsletter.

Skeptical Brifes is published four times a year to the Associate Member of Committee of Skeptical Inquiry, a skeptic organization dedicated to promote skepticism and science. This organization also publishes the famous skeptical magazine Skeptical Inquirer.

My first column was the interview I had done with evolutionary biologist Jerry Coyne (available here). He posted about it on his site, as the images below shows.

It's interesting to see that Coyne said was prepared for the interview: "... Brazilian writer Felipe Nogueira who was clearly well read about my stuff". 

One reader of Coyne's website said the questions were great, especially the question "Mayr vs Dawkins"

Sunday, April 13, 2014

Assessment of Homeopathy by NHMRC

by Felipe Nogueira

Homeopathy is type of complementary and alternative (CAM) medicine based on two principles. The first, "like cure like", states that substances can be used to treat the same symptoms they cause. The second principle is the potentisation: the substance is diluted and agitated several times. Homeopaths use the C notation to indicate that 1 part of the substance was diluted in 100 parts of water (or alcohol). Then, 200C, used in the prepation of Oscillococcinum, indicates that, firstly, 1 part of the substance was diluted in 100 parts of water. After that, 1 part of the result of each dilution was diluted in 100 parts of water until it totalizes 200 dilutions. This means that, by the end of 200 dilutions, 1 part of the original substance was diluted in 100200 parts of water. Homeopaths called this process potentisation because they believe - as crazy as it sounds - the more diluted the homeopathic preparation, more strong it is.

The National Health and Medical Research Council (NHMRC), as stated on its website, is Australia’s leading expert body promoting the development and maintenance of public and individual health standards. Its mission is working to a make a more healthy Australia.  

Recently, NHMRC realized a big assessment of the evidence of the effectiveness of Homeopathy. This assessment had been done because is NHMRC's role to provide the best evidence to help australians to make health decisions. And this includes decisions regarding the use of CAM. NHMRC published a draft for public consultation*. Any aditional evidence may be submitted for analysis until the end of May. 

Evidence analysed by NHMRC
As described on the draft, the assessment objective is to answer the question "Is homeopathy an effective treatment for health conditions, compared with no homeopathy, or compared to other treatments?". To achieve that goal, NHMRC considered 57 systematic reviews that assessed the effectiveness of homeopathy for tretating 68 health conditions. It is important to highlight the following:
  • NHMRC considered "evidence" only prospective and controlled studies in humans; it does not included individual experience, testimonials or case reports, or research that was not done using standard methods
  • NHMRC considered papers submitted by the public, Australian Homeopathy Association and Australian Medical Fellowship of Homeopathy
  • NHMRC did not consider evidence whether or not homeopathy is effective for preventing health conditions or whether it's good for general health. 
Homeopathy compared with placebo
The systematic reviews considered by NHMRC found studies that compared homeopathy with placebo for 55 health conditions.

For 13 health conditions, it was found that homeopathy was reported to be not better than placebo in at least the large majority of reliable studies (well-done and with enough participants). These conditions were: adenoid vegetation in children, asthma, anxiety or strees-related conditions, diarrhoea in children, headache and migraine, muscle soreness, inducing or shortening labour, pain due to dental work, pain due to orthopaedic surgery, postoperative ileus, premenstrual syndrome, upper respiratory tract infections, warts.

For 14 conditions, some studies reported that homeopathy was more effective than placebo, but NHMRC considered those studies not reliable, because they were not well done or had too few participants. These conditions were: allergic rhinitis, attention deficit/hyperactivity disorder in children, bruising, chronic fatigue syndrome, diarrhoea in children, fibromyalgia, hot flushes in women who have had brest cancer, HIV infection, influenza-like illness, rheumatoid arthritis, sinusitis, sleep disturbances or circadian rhythm disturbances, stomatitis due to chemotherapy, ulcers.

For 29 health condition, only one study that compared homeopathy with placebo was found. These studies were considered not realible, because they were poor or unknow quality, or they had too few participants It was not possible to make any conclusion about whether homeopathy was effective or not for these conditions that were the following: acne vulgaris, acute otitis media in children, acute ankle sprain, acute trauma, amoebiasis and giardiasis, ankylosing spondylitis, boils and pyoderma, Broca's aphasia in people who have had a stroke, bronchitis, cholera, cough,  chronic polyarthritis,  dystocia, eczema,  heroin addiction, knee joint haematoma,  lower pack pain, nausea and vomiting associated with chemotherapy, oral lichen planus, osteoarthrits, proctocolitis, postoperative pain-agitation syndrome, radiodermatitis, seborrhoeic dermatitis, supression in lactation after childbirth in woman who elect not to breastfeed, stroke, traumatic brain injury, uraemic pruritis, vein problems due to cannulas in people receiving chemotherapy. 

Homeopathy compared with other treatments
For 8 conditions, some studies reported that homeopathy was more effective than Placebo. NHMRC considered those studies not reliable, because they were not well done or had few participants. Those conditions were: acute otitis media or acute otitis media with effusion in children, allergic rhinitis, anxiety or stress-related conditions, depression, eczema, non-allergic rhinitis, osteoarthritis, upper respiratory tract infection. 

For 7 conditions, only one study that compared with homeopathy with placebo was found. These studies were considered not realible, because they were poor or unknow quality, or they had too few participantsFor these conditions, it was not possible to make any conclusion about whether homeopathy was effective or not. These conditions were: burns (second and third degree), fibromyalgia, irritable bowel syndrome, malaria, proctocolitis, recurrent vulvovaginal candidiasis, rheumatoid arthritis. 

Studies that were not found
The sytematic reviews considered by NHMRC searched but didn't find studies for the following 7 health conditions: borderline personality disorder, dementia, constipation in children, glaucoma, nocturnal enuresis, lower urinary tract symptoms in men, and chronic facil pain. 

The conclusion by NHMRC is very clear and can be read on the page 10 of the draft's document: 

NHMRC concludes that the assessment of the evidence from research in humans does not show that homeopathy is effective for treating the range of health conditions considered. 
There were no health conditions for which there was reliable evidence that homeopathy was effective. No good-quality, well-designed studies with enough participants for a meaningful result reported either that homeopathy caused greater health improvements than a substance with no effect on the health condition (placebo), or that homeopathy caused health improvements equal to those of another treatment.  
NHMRC published four very detailed documents*. The systematic reviews considered were extensively discussed on those documents; the forms for assessment of the quality of each study were published. These information are all avaiable on-line.  Not surprisingly, Edzard Ernst, the first professor of CAM in the world, considered the NHMRC's assessment the most through and most independent in the history of homeopathy. According to Enrst, this assessment merged two perspectives on homeopathy - skeptics' and evidence based medicine advogates' - isolating the believers and rendering their position no longer tenable. I don't think I need to say anything else besides the following comment by Ernst:
it appears more and more as though homeopathy is fast degenerating into a cult characterised by the unquestioning commitment and unconditional submission of its members who are too heavily brain-washed to realize that their fervour has isolated them from the rational sections of society. And a cult is hardly what we need in heath care, I should think. It seems to me therefore that these intriguing developments might finally end the error that homeopathy represented for nearly 200 years.
All documents published by NHMRC regarding its assessment of homeopathy can be found here

Wednesday, February 12, 2014

Jerry Coyne: "The theory of evolution has been confirmed as true over and over"

by Felipe Nogueira

Interview with Jerry Coyne
Jerry Coyne is an evolutionary biologist, Professor in the Department of Ecology and Evolution at the University of Chicago. He is also a member of the Committee on Genetics and the Committee of Evolutionary Biology. 

Coyne is a big popularizer of evolution and science. His lastest book is Why Evolution is True, where he shows with clarity the several evidence supporting the theory of evolution and debunks many creationists arguments. 

I did an interview with him that is available on Youtube. This is the first part of the interview. I think having this post, the part of the interview we talked about several things about evolution (misconceptions, evidence, mechanisms), published today it's a good way of celebrating Darwin Day. I thank Jerry Coyne for his attention and kindness.  

Can you explain why evolution is not just a theory?
It’s a theory and a fact. As I explain in my book, theory in science has a different meaning from what most people think of. I think that was used in debate between Ken Ham and Bill Nye. Someone in the audience said evolution is just a theory, implying it is just a guess or speculation. In science, a theory is a proposition or an explanation that purports to draw together a number of facts to explain a phenomenon. So, we have the theory of gravity, the germ theory of disease, for example. Or the atomic theory: matter is made by constituents called atoms. Atoms are facts. In the same way, evolution is called a theory, because Darwin proposed explanatory mechanism for all these diverse facts. So, evolution like the atomic theory or the germ theory of disease is both a theory and a fact at the same time, but a theory in scientific sense, which is a well-established explanation for a diverse group of phenomena. And again this is probably the most perverse misconception about evolution, at least in America.

I think you already answered my second question. You mentioned very clearly on your book that the theory of evolution is not just the statement the evolution had happened; it includes explanations why and how evolution happens. 
It’s the statement of what has happened and why has happened. [The paleontologist] Stephen Gould made that pretty clear, although he thought that a theory was the explanation why and the fact was the thing itself. It’s a matter of taste how you called a theory, but it’s not a matter of taste that theory of evolution is something that has been confirmed as true over and over again, and that what is important to emphasize when you came up with this misconception.

But the words “theory of evolution” are equivalent to “modern evolutionary synthesis”? 
The theory of evolution that I talked about in my book is the one most people hold, pretty much the one Darwin proposed, which involves elements of evolution, gradual transformation of population (genetically, although Darwin didn’t know genetics), splitting of lineages, so you get one species forming more, so you have a branch tree of life, and that gives the result that any pair of species has a common ancestor and that the organisms look like they are designed, which is the result of natural selection. So that is a Darwinian theory of evolution. Neo-Darwinian theory is based on genes and there is other process like genetic drift and horizontal gene transfer. They are important, and they have been confirmed as true, but for the average person who disbeliefs evolution, what they are disbelieving is those five propositions I just outlined. 

What do you think is the most common misconception about evolution? 
One is that is very common in children involves instantaneous transformation of population, like every individual turns into something else rather than a gradual genetic change in the composition of the population. Another one is that there is not much evidence for it, that we don’t have the evidence for one type of animal turning into another over time. But the fact is there are lot of evidence, people just don’t know about.  

One of the misconceptions is that evolution is just a random process. 
That’s a good one: “how all this can happened by chance?” Is easily dispelled if you understand what natural selection is, but it is very common. And in America it's connected with all kinds of religious things, like if you believe in evolution, you have to give up of your morality. That’s probably the main reason why religious people oppose evolution in America, and maybe Brazil as well, because it is religious country. They say "what basis do you have to be moral, if you are just an evolved animal, like a chimpanzee?" And that’s a misconception as well that comes from a misunderstanding of where morality really comes from. 

And there is the misconception of the definition of the word random in the context of random mutations.  
The average person is not sophisticated enough to know that mutation is a random process and less of them know what we really mean by random process, which is the occurrence of mutation is indifferent of its effects on the reproductive outcome of its carriers. That is probably most common among more sophisticated creationists. I don’t think it’s a misconception, I think it’s deliberate, it's something they say to make people question evolution, which is their mission  

There is also the misconception of “the missing link”; it’s not just one missing link, it’s a lot of them.  
That is a misconception of what a missing link really is. The missing link between human and chimps would be the common ancestor between human and chimps. That is a single species that split into the two populations: one which gave rise to hominids and the other gave rise to bonobos and the chimps. We generally not going to find a single species in the fossil record, but you don’t need the missing link to prove human and chimps have a common ancestor. You need, as I tell in my book, is if you go back earlier and earlier in the human lineage you would expect to find more and more transitional forms that show ape-like ancestor and, in fact, that’s what you find.  Ken Ham said the same statement in the debate last night: “we have evolution within kinds: dogs evolve into other dogs, but we never see a dog evolving into a cat”. But if you look in the fossil record, you see these transitions: Tiktaalik, which Bill Nye mentioned, is a transitional form between fish and amphibians; we have between amphibians and reptiles; the reptiles and mammals, the so called “mammal-like reptiles”. I mean, there is a very good fossil record there. We have between reptiles and birds, what a great collection of transitional forms we have on the feathered dinosaurs; between whales and theirs terrestrial ancestors, and of course all the transitions in the human lineage. We have not only the links between major types of animals that were predicted by the theory of evolution and there also the links between the so-called different kinds the biblical creation says could not exist. Those kinds of fossils absolutely dispelled any kind of creationism.

What about those creationists/intelligent design proponents’ ideas that the wing or the eye is too complex to appear by gradual changes over time?
Darwin was the first one to deal with the eye in The Origin, showing we have all degrees of eye development in living species and there is no problem envisioning how you go from one to another. Secondly, we have this paper by Nilsson and Pelger in Proceedings of The Royal Society*. They made a simple model of the evolution of a complex camera eye from a light sensitivity eye spot, like you have in plenary worms. They made very conservative assumptions about what mutations rates might be, about what the selection pressures are, and in few thousands generations they saw this eye spot evolve into a complex eye. So, we have two kinds of evidence that dispel the idea the eye is too complex to evolve. We have a sequence of eyes in living creatures which you can plausibly connect, showing how they can straight up. Second, we can make the process happen through computer simulation using conservative assumptions. And that goes to every other complex feature; the blood clotting is another one that intelligent design people use. They say “how can you get this complex cascade of enzymes reactions that results in a blood clot? It can’t possible evolve, because, if take out any intermediate step, the blood won’t clot. So, all got to be there and God did it”. But research show you can knock-out certain intermediate steps and still get clot. We don’t know how it happened, because we weren’t there, but you don’t need to actually observe it to reject creationists arguments that it is too complex to evolve. All you have to show is that you make a plausible scenario, where each step has adaptive advantage to show that evolution was plausible. And we have done that for almost all these traits that is supposedly non-evolvable and too complex.

Richard Dawkins’ The Selfish Gene focus on the gene centered view of evolution. But I think the evolutionary biologist Ernst Mayr was a critique of that view. What is the current accepted view of the target of selection? 
When you use the words “target of selection”, you are sort of anthropomorphizing the process, because selection is not some force that is out there. What we mean is what is unit of differential reproduction causes evolution. I think Dawkins is generally right. In almost every single case that we know of, we can reconstruct what happened and see the basis of evolutionary adaptation, and it’s basic the gene itself. Insecticide resistance in insects is a resistance against organophosphate insecticide and in many cases is the same gene, because we can localize where the lesion is on the gene that actually is causing resistance. In many cases, it is the exactly same mutation in different insects. That and in other many cases that we manage to localize where selection started, it’s on the gene level. That said, that are conceivably other targets of selection. Group selection, many have said as a plausible alternative, that is, it’s the group that has the differential reproduction. That’s been used to explain things from the evolution of altruism to sex. First of all, groups don’t proliferate and go extinct and fast as the individual. Second, I can’t think of an adaptation that is good for the group, but bad for the individuals, which you would expect to see if group selection occur overriding individual selection. I think Dawkins is pretty much right: the thing that has to change to cause evolution is the gene, but it does that by affecting the reproduction of the individual that carries that gene. In that way,  you can see the target of selection as the individual. You can think of the gene as the replicator, and the individual whose reproduction is affected by interacting with the environment as the vehicle for the gene .

Mayr was even critic of the definition that evolution is the change in the gene frequency. 
Most people think of evolution as observable changes in the organism over time, like dinosaurs evolving into birds. But, of course, that means there was a change in the frequencies of the genes. I prefer to look to evolution as the changes in the gene frequency, because you can have changes in phenotypes over time that aren’t what we called evolution. For example, the Japanese population has increased at least 6 inches in height, since the World War II, because the improvements in nutrition. I don’t think we called that evolution. Some people would, because they think evolution is change. But for biological evolution, which is what are talking about, ultimately you have to take that back to the gene frequency, because the Japanese population increase in height is not an example of biological evolution. I think Mayr was hanging up in a semantic there, because, after all, Mayr explicitly admitted to me “I don’t know anything about population genetics”. So, he preferred definition that comports more of his area, which is looking at phenotypic change.

You had mentioned the importance of other mechanisms other than natural selection in evolution, such as the genetic drift and sexual selection. What is their importance?  
Sexual selection is natural selection; it is a specific form of natural selection that involves mating. I don’t break that of from natural selection, but some people have tried to that. E.O Wilson tried to called it a separate evolutionary process. But it’s not, it’s the same thing. Genetic drift is a random change in the frequency of the genes due to stochastic reproductive differences, such as the differences in the sex ration, and differences in the number of offspring, that don’t have anything to do with fitness. The question is how important is it. That’s a question I liked to ask graduation students in qualifying exams. And the answer is probably important in molecular evolution, because there are lots of characteristics in molecular evolution that its change don’t affect fitness, such as the parts of the DNA that don’t do anything, so-called “junk DNA”. So, genetic changes in those regions are probably going to evolve only by genetic drift, because they can’t affect the reproductive outcome of the carriers. In the context of evolution of phenotypes, it is hard to prove that a trait evolved by genetic drift rather than selection, given that a tiny selection advantage can cause change over millions of years and you can measure that. The higher frequency of some deleterious genes in human populations like the Dunker and the Amish, the higher frequency of disease genes in Ashkenasi Jews can probably be attributed to genetic drift as well. But it is hard to given an example of that process operating in the observable traits of organisms. Probably operates, we just don’t have many good examples of it. There is also meiotic drive: when we have two different copies of the gene, when it’s time to make eggs and sperms, one copy kills the other one and that is represented in the next generation. But you can think of that as a kind of selection as well, although is not adaptive selection; it’s differential reproduction of the gene, it doesn’t make its carrier any better fit, in fact, it causes population to go extinct.  So, the two big forces of evolution are the deterministic force of natural selection and random force of genetic drift.
People think the only evidence we have for evolution is the fossil record, but even without the fossil record, evolution is true. So, what are the other ways to corroborate evolution? 
I think Dawkins made that point. We have enough evidence from other areas that we could document evolution without the fossil record. The evidence we have showing the organisms are related; the embryological data, that only makes sense in the light of evolution; the biogeographic data, which I described in my book, is very powerful evidence for evolution; vestigial organs; the existence of vestigial genes, the human genome has genes for making egg yolks and yet we don’t do it, those genes were inactivated. How do you explain that, unless we evolve from organisms that originally did make egg yolks, which we did? Ten years after Darwin, almost every biologist and rational lay person accepted evolution and yet there was no fossil record that actually showed evolution. But for many people the fossil record is the most convincing. When you can really show them a feathered dinosaur, that kind of evidence is very powerful. 

* This paper is “A Pessimistic Estimate of the Time Required for an Eye to Evolve” authored by Dan-E. Nilsson and Susanne Pelger published in Proceedings of The Royal Society of London, Series B, 256, 53-58, 22 April 1994. The paper abstract is available on the link:

Jerry Coyne: "If you accept science but rejects it where it conflicts with your faith, I don’t think you are behaving fully scientifically"

Jerry Coyne is an evolutionary biologist, Professor in the Department of Ecology and Evolution at the University of Chicago. He had written a book about the evidence for evolution titled Why Evolution is True. He has a blog with that name, where he posts about science in a daily basis.  This is the second part of the interview I did with Jerry Coyne.

Links: first part | video on Youtube | versão em português

How does religion create a barrier to understand evolution? How can we solve this problem? 
In your country [Brazil] it’s a lot less of problem than in mine. You country is catholic and the official position of the Catholic Church is that evolution is ok. But they have some positions which are explicit anti-evolutionary. One of them is that Adam and Eve is real people; we all descended from Adam and Eve. We know now the human population ancestor of modern humans could not have been small that 2000. That causes a problem among Christian in the US, because that not only undermines Catholicism, undermines any form of Christianity whose beliefs depends on Jesus coming back to save us from the sin committed by Adan and Eve. If Adan and Eve didn’t exist, then there is no original sin, so what’s the point of Jesus? Catholics also think, and Pope said this, that humans are different from other creatures because God gave us a soul. Where is this soul? When did it come on human lineage? What’s the evidence that it exists, if there is any? Catholics accepts evolution, except for two things: God had a hand in human evolution and human evolution involves Adam and Eve. If you accept science but rejects it in those areas where it conflicts with your faith, I don’t think you are behaving fully scientific. So, the Catholic’s position on evolution is better than American Baptist, but still opposes to science, because it gives up on science, when science comes into conflict with the catholic dogma and that’s not a good way to behave, because prioritizes faith over evidence, over rationality.  In the US is much worse, because 46% of America rejects evolution. That because our country is religious, probably more than yours [Brazil], but religious in a different way because they are not Catholics, they are protestants and a lot of protestants simply don’t believe in evolution. And 23% of American Catholics don’t accept evolution neither; they are young-earth creationists. They violate the tenets of their own church.

What about the incompatibility of science and religion? You have written about it, so what’s your opinion on that? 
I’m actually writing a book about that. What I mean by incompatible is not that scientists can't be religious, this is true, a lot of scientists are religious, like Francis Collins. Or that most religious people don’t accept science because they do. What I mean by incompatibility is the methodology the science uses to find out things that are true about the world is an exact opposition to the methodology that religion uses. That claim rests on my contention that religion does make factual claims about the world and I can document that. Some of the factual statements Catholics believe are that Jesus was their savior, he was the son of God, he died and was resurrected, and he is going to come back and we’re all going to have an after-life, except for the bad ones that will burn in hell. Those are real statements about what is true about the cosmos that is being overseen by some bodyless mind that has a personal relationship with us and who hears our prayers. The scientific attitude towards that is “I am not going to believe until you show me the evidence”. I mean, prove to me there is a heaven, and you can’t. So, scientists say since there is no evidence for heaven, I am not just going to accept it. That is not saying I know there is no heaven. When you’re an atheist like I am, you don’t say I know there is no God. That’s not a scientific attitude. What you should say is I don’t see any evidence for God, so I am not going to accept that. Just the same way people say I don’t see any evidence for fairy or leprechauns, so I am not going to accept it, and everybody is like that, but when it comes to God and there is the same lack of evidence, instead of saying I’m not going to accept it, they say “well, it could be true, we just don’t know”. The scientific attitude towards claims about what is true about the cosmos demands evidence, demands consistent evidence, that everybody agrees on that, it demands testability, either observational or historical, and doubt and replication. That’s all true of science, but none of that is true of religion. The ultimately proof that religion doesn’t really tell us the truth about the cosmos is that we have over 10.000 different religions that makes different claims about the universe that are conflicting. Islam thinks if you see Jesus as your savior, you´re going to hell, and a Baptist is going to say that if you´re a Muslim and don’t accept Jesus as the prophet, you’re going to hell. If faith, dogma and authority were the correct way to find truth about religious matters, all religion would have the same tenets. The fact is that faith, dogma and authority – which are the tools religion uses to find truth – can’t find truth. That means truth finding of religions people are incompatible with scientists.

You have been critic of accommodationism and said it does not work. Why? 
One example is how the Catholics are accommodationists.  Catholics is one the most science friendly and they accept evolution. But there are certain things they have to accommodate, one of them is Adam and Eve. The bible says Adam and Eve existed, they were the cause of the original sin, and Jesus will come back. How the Catholic Church accommodates that? It doesn’t, it says that their dogma is that Adam and Eve is real people and gave rise to ancestry. That is in direct conflict with what the scientific data tell us. So, Catholics rejects science. In fact, 64% of America said in a poll taken about seven years ago that if there is a fact in conflict their religion, they would reject the fact, rather than reject their belief.  Accommodationism doesn’t not work. There is Stephen Gould approach of NOMA [non-overlapping magisteria] that religion does not make any claims about the world and science should let religion handle the issues of morality, meaning and values. That fails on both counts, because religion does make claims about the world, which are testable in some cases, and meaning, morals and values can be handle by a secular perspective; the ancient Greeks have done this, many philosophers do today.

I think Science can tell us a lot about our morals.
It can say a lot more about morals that people can think it can. One of the people that is actually engaged in this is [primatologist] Frans de Waal. He had written a book about the evolutionary origins of morality. Our instinct moral feelings are designed to care for our children. de Waal had showed that social primates and other animals have behavior that are remarkably. Also [psychologist] Paul Bloom that showed that children before they can speak show sort of innate moral stimuli, empathy, caring for those you're familiar with and sense of fairness. There is a remarkable video that to me shows the chimps have sort of innate sense of fairness, which young infants have as well before they socialize. I think that sense of fairness is in our genes. This kind of scientific anthropological and developmental exploration tells us something about our morality. They can’t tell us what is right, I still believe that, in oppose to Sam Harris. I don’t think science can tells us how to behave. I think we should be helping people at Africa, which we're not really related at all.   

I'd like to thank to professor Coyne for his time and kindness.