Tuesday 25 March 2014

Intelligent Design

There is a lot of confusion and misunderstanding, and not a little misrepresentation, about the theory of intelligent design (ID) out there, especially on certain web sites. Those who do not like some of the supposed implications of ID choose to equate it with "creationism", which they usually take as a simplified literal reading of the first two chapters of Genesis in the Bible. Some even claim that ID is somehow not even a scientific theory. Others who support such a literal reading (the true "young-Earth, six-days creationists") often apply the findings of ID research in a misplaced attempt to bolster their own pseudo-science arguments, thereby sowing further confusion. Both approaches are false, so to clear the air by some small amount, as a believer in the ID theory, I will try to explain it.

Intelligent Design is a theory about origins: the origin of the cosmos, life on Earth, and the wide variety of life we find around us today, including ourselves. On these subjects, there are only two basic possibilities: either our origins somehow involved a mind (AKA the intelligent designer, or possibly "creator") having purpose and planning, or else they did not and the universe and life came about with no purpose and no plan or guidance -- two options if you will, mindful or mindless!

Materialists -- those who believe that matter and energy are all that exist -- rule out the mindful option (and any form of ID) a priori, without even considering it. But that seems unreasonable. Surely it is at least conceivable that there is a Creator of some sort that was somehow purposefully involved in putting together the universe and getting life started on this planet? If so, wouldn't exploring that option be a useful endeavour?

Supposing for a moment that there was a Creator that brought the Universe, or life, or us into being. One might then expect that there would be some evidence of his (or its) activity left behind in the world around us. This is what ID researchers claim to have found by various types of scientific study. They have examined evidence in physics and biology and claim that the best explanation for some of what we see is the work of an intelligent agent doing what we would normally refer to as "design"; i.e. purposeful selection and assembly of components for a complex item with defined function.

There are other sciences that look for the effects of intelligent agents; archeology, espionage, criminology and forensics all try to explain historical facts to determine whether an intelligent agent was involved. Add to this the SETI research looking for meaningful (i.e. purposeful, complex, non-natural) signals from other star systems as evidence for extraterrestrial intelligence. Given that we can often distinguish natural and intelligent causation in these fields, why not do the same for research into origins?

ID presents two types of evidence. Some is positive evidence; e.g. the incredibly fine tuning of the fundamental physical constants and initial conditions of the Universe, which together allow elements, stars, planets, life and people to exist; or the extensive, complex and highly-functional information coded into the DNA in every living cell; or the complex interacting and self-regulating nano-machinery inside these same cells. Some of the evidence is negative; if there are really only two alternatives, then evidence against one of them (materialism) may be counted as evidence in favour of the other (ID).

In this latter category we have the abiogenesis of life on Earth, which no materialist hypothesis comes anywhere close to explaining in a credible way. We also have the Cambrian explosion and most of the fossil record showing fully-formed complex life forms coming into existence without intermediary precursors, contrary to the expectations of Neo-Darwinism; the materialist theory for the evolution of life. Then there is the failure to produce a unique "tree of life" based on the DNA in present life forms, and of course, there are the "irreducibly complex" structures in some cells which are not explicable by the Darwinian mechanism, which allows no foresight or purpose.

Some of the ID studies, experiments and analyses demonstrate the complete inability of Darwinism (i.e. unguided mutation plus natural selection) to produce new proteins and physiological structures as life develops and new species come into being. Many non-ID scientists now agree that Darwinism cannot explain much of what we find in the fossil record and in living species. Materialists keep trying to find naturalistic ways around these failures, but so far have come up empty as far as testable theories go.

On the other hand, ID accepts the role of Darwinism where it can reasonably be applied; in bacterial resistance to antibiotics, for instance, where a single amino acid knockout explains the loss of bacterial function used to prevent the antibiotic from working. But ID research also finds evidence that, when examined with an open mind, points to the work of an intelligent agent as the best explanation.

Intelligent design is a scientific theory, doing experiments, writing papers, involved in conferences and discussions, and making predictions. For example in the 1980's ID researchers predicted that the non-protein-coding DNA between genes in the chromosomes of all living species would be found to have important functions. Materialists dismissed these nucleotide sequences as "junk DNA" and loudly proclaimed them as "proof" of Darwinian evolution -- the waste products of random mutation left behind in the genome. This slowed research into the vast majority of the genome, but recently numerous purposes have been discovered for this "junk" and now it seems that most, if not all of your DNA is important to control your development, differentiate cell types and manage the expression of the genes that code for proteins. ID has made other predictions and opened up avenues for research.

Just to be clear, ID accepts various aspects of "evolution"; the changing life forms over millions of years as revealed in the fossil record; and micro-evolution with shifting ratios of different alleles in a population that explain changes in colouring, beak sizes, etc. ID is also compatible with the concept of common ancestry for all of life, even as it uncovers evidence that brings that concept into question. Therefore, arguments for these aspects of evolution cannot be used to argue against ID. What ID does argue against is the Darwinian attempt to expand micro-evolution to the macro level to explain new body plans and novel protein complexes. There are areas for both agreement and disagreement, and anyone seeking to study origins should examine all aspects and both sides of any apparent conflict.

As a science theory, ID does NOT claim to identify the intelligent designer. Just as a criminologist, armed with forensic evidence, can conclude that a particular death was a murder (i.e. caused purposefully by an intelligent, if rather misguided, agent), without identifying the murderer, so can ID find evidence of intelligent causation without having to name the designer. Of course, given the scale of time and the nature of the origins events, the obvious candidate is God, but that supposition is not a result of the ID science, and to claim otherwise is disingenuous.

ID is sometimes dismissed as a "god of the gaps" argument, wherein "god" is invoked to account for areas that science has not yet been able to explain. However, this too is a misrepresentation. As science delves deeper into various aspects of biology, more "gaps" in Darwinism appear, making it harder to believe, and more evidence accumulates that the basis of life is information, which in our experience, is best explained by the action of an intelligent agent rather than mindless chance and physical necessity. When presented with widening gaps in our knowledge and presumed explanatory powers, it is best to consider ALL possible explanations and look for the one that best accounts for the evidence, rather than dismissing one out of hand just because it does not fit some preconceived ideas about reality.

There are many web sites, videos and books that explain ID, and present the detailed evidence in its favour. For careful and civil discussions about ID and the latest findings, I suggest looking at: http://www.evolutionnews.org/ . There are other good sites, and of course there are pro-Darwinism and anti-ID sites as well, which you are welcome to peruse. But don't study only one side as you will get a skewed view of reality. Check out several and see how credible they are, even if you do not fully understand all of that you read. The exploration is fascinating and the controversy is stimulating.

In summary, Intelligent Design is a bona fide scientific theory that claims to have found evidence for design in nature. Before writing it off and pooh-poohing the IDea, it would be better to take a look at the evidence with an open mind and assess it fairly. Isn't that what science is supposed to do?

Wednesday 19 March 2014

Epidemiology 100

Some simple mathematical thoughts about epidemics. An epidemic is a disease that spreads rapidly or expands into a large population. A bit of thought will show that for a disease outbreak to become an epidemic, each person with the disease needs to pass it on to more than one other person on average. Suppose 100 people have the disease but on average each one has only a 50% chance of passing it on to another person before the disease runs its course. In that situation an epidemic is impossible; the original 100 will pass it on to only 50 new sufferers, who will pass it on to only 25 new cases, and so on until the disease stops with only 200 (approximately) having been affected. Not an epidemic.

If on the other hand, each person on average passes the disease on to two others, then there will be exponential growth and a real epidemic unless it is contained by some intervention. In that case, the original 100 sick people will infect 200, who will pass it on to 400 new cases, and so on. Thus, it is useful to think in terms of a "infection ratio" being the average number of people each affected person infects before the disease has run its course.

Clearly various factors will affect this infection ratio for different populations, subgroups or even individuals. Things like the weather, the population density, living conditions, sources of food and water, etc. can all change the circumstances of infection and hence the likelihood of transmitting the disease. Perhaps the most obvious factor is vaccination. In a population where almost everyone has been vaccinated against measles, there is little danger of one case of measles causing an outbreak. On the other hand, as the unvaccinated fraction of people increases, the danger of an outbreak will rise, until the infection ratio exceeds unity. Then an outbreak will occur, which could turn into an epidemic unless measures are taken to reduce the infection ratio, by vaccinating all the unvaccinated people, or perhaps just by isolating the sick people from contact with unvaccinated ones.

One interesting application of this concept is HIV infections in North America. Under typical conditions, faithful monogamous heterosexual people who do not inject drugs with shared needles have a very low chance of contracting HIV, and if they do contract it by some means, they have a low probability of passing it on to anyone else, or perhaps at most, to only one person. Thus, HIV/AIDS in such a population would never have become an epidemic.

In contrast, there are at least two groups in North America with demonstrated HIV infection ratios above unity. These are injection drug users (IDU's) who share needles, and men who have sex with other men (MSM). In both cases, the behaviours of people in these groups raise their infection ratio above unity, and the virus infects others in those groups. Indeed, these two groups remain the two where HIV/AIDS is most prevalent, and most of the new infections (on a per capita basis) occur.

For IDU's, sharing needles transmits the virus from one individual directly into the bloodstream of another. Since such people shoot up often, and sometimes change who they do it with, the risk of infection can be very high and the disease can spread rapidly in that population. Therefore preventive measures like needle exchanges, or bleach washing of used needles can be important to reduce the risk and stop the epidemic.

With MSM, the combination of anal sex and multiple partners make HIV transmission much more likely than for single-partner, heterosexual intercourse. Thus, here too, the infection ratio can be quite high and the virus can spread quickly through an unprotected population.  For example, recall "patient zero" and the rapid increase in AIDS among homosexual men before the virus was identified. Here too, limiting partners, and using some form of protection can presumably reduce the risk.

Notwithstanding attempts to prevent transmission and limit the risk of infection, these two populations remain centres for HIV transmission in the North American population. Indeed, these two sub-populations may be considered as "reservoirs" for the disease and act to maintain it at significant levels within the wider population. How that works can be explained by the relative infection ratios of these two groups compared to the rest of the people. Within these sub groups, the infection ratio is high (more than one), so the disease does not die out.

However, these groups also interact in risky ways with people outside their groups, and thus may pass on the infection to those people. For example, bisexual, or secretly homosexual men may infect their female partners, even if the chance for that is relatively low. In the past, IDU's might give blood to earn money to pay for their drugs, children might be pricked by used needles left in parks, or health care workers might accidentally get infected blood on them.

In such ways, HIV/AIDS can "leak" out of the reservoirs where it is sustained, and into the broader population. But once there, it does not become epidemic, because the subsequent infection ratio outside the reservoirs is less than unity. A few other unfortunates will contract the disease, but for most of us the risk is low, although given the nature of the disease, taking precautions in uncertain situations is still a good idea.

This analysis suggests that efforts to combat the spread of HIV/AIDS should focus almost entirely on the reservoir sub-populations of IDU's and MSM. This is happening to some extent, but misplaced political correctness (e.g. "everyone is at risk" campaigns), and the tendency of these two groups not to adopt the recommended precautions (any needle for a fix?) allow the reservoirs to maintain the disease at low but stable levels, condemning many more each year to the AIDS disease.

Stronger methods (recall the "Typhoid Mary" quarantine rules) could be applied if health care agencies had the will and political clout to apply them. Mandatory HIV testing for some groups, tightly focused educational campaigns, backed up by strong laws against knowingly transmitting the virus, enforced and coupled with aggressive treatment regimes, could presumably reduce the infection ratio even within these reservoirs, thereby winding down the disease, at least to some significant degree.

Given the cost of lifelong anti-HIV treatments and the poor health associated with the disease and ongoing treatments, it seems that we would be well advised to pursue such measures, to protect these sub groups and the population at large from this scourge. There are good reasons for being sexually faithful to one partner, and for not injecting yourself with drugs, and North America would do well to promote truly healthy behaviour and stop pretending otherwise. I expect an unbiased professional epidemiologist would agree.