Atherosclerosis is better known as "hardening of the arteries". It involves a build-up of cholesterol laden plaque along the inside of your blood vessels. Atherosclerosis sometimes leads to bits of plaque rupturing into the blood stream, blocking blood flow, and causing a heart attack or stroke. These mechanisms, at their macroscopic level, are well understood. Post mortem, researchers can measure the plaque, find the rupture, find the clot, see the dead heart tissue, etc. But are you willing to believe that what causes atherosclerosis is not understood?
Since the mid-eighties the "lipid hypothesis" of plaque formation has been more or less accepted as medical dogma. "It has been established beyond a reasonable doubt that lowering definitely elevated blood cholesterol levels (specifically, blood levels of low-density lipoprotein (LDL) cholesterol) will reduce the risk of heart attacks caused by coronary heart disease."  Soon statin drugs became the norm to lower blood cholesterol levels and prevent heart attacks. The results were encouraging.
In addition to drugs, research found that if all cholesterol and fats are cut from the diet then levels of cholesterol in the blood drop and fewer heart attacks occur in people who have already had a heart attack.
Cholesterol is mainly found in saturated fats. Thus saturated fats are routinely singled out as dangerous for people to eat.
The NIH website states," How does cholesterol cause heart disease? When there is too much cholesterol in your blood, it builds up in the walls of your arteries."  Simple. Perhaps too simple? Indeed, this theory is being questioned by small groups around the world.
THINCS is The International Network of Cholesterol Skeptics. They believe that "enormous human and financial resources have been wasted on the cholesterol campaign, [while] more promising research areas have been neglected."  They contend that there are numerous reasons to look at other theories for the cause of atherosclerosis and heart disease. Normal scientific practices involve dissent and discussion but THINCS thinks that the lipid-hypothesis is not open to the scrutiny or questioning that it should be.
This unquestioning belief in the cholesterol campaign means researchers like Uffe Ravnskov, a Danish medical doctor, have difficulty getting published. "Dr Ravnskov has received the Skrabanek Award in 1999 from Trinity College, Dublin, Ireland, for original contributions in the field of medical scepticism. He was also honoured with the Integrity In Science Award 2003 given by The Weston A. Price Foundation."  Infamous for his views against "The Cholesterol Myth" he is often quoted and often attacked around the 'net.
Ravnskov states," No study of unselected individuals has found an association between the concentration of LDL or total cholesterol in the blood and the degree of atherosclerosis at autopsy." 
But how can he say this? The secret is in the word "unselected". What it boils down to is quite simple. The connection between cholesterol and heart disease is clear. The causation is not. Studies have consistently shown that people with heart disease have cholesterol problems. This isn't refuted. But the connection between eating cholesterol and falling ill with heart disease is assumed by the current scientific consensus. What Ravnskov says is that if you look at healthy people and their cholesterol levels there is no statistical connection to their rates of heart disease.
Most science is based on random studies, sampling as much of a population as possible. However the work on heart disease has centered on studying people who have it already, not on why other people don't have it.
Amongst his many works, Ravnskov even has alternate theories that explain the cholesterol connection and the causation of atherosclerosis.
Prior to general acceptance of the lipid hypothesis, researchers and doctors believed that plaque formation in the arteries was caused by infections in the body. Post mortem research showed direct correlations between arterial plaque build-up and long term sickness. People who had died after long illnesses had extensive plaque build-up and people who died after shorter illnesses had less plaque. 
Ravnskov believes there are multiple reasons to look at infection as a cause or contributor to atherosclerosis and heart disease. He believes that cholesterol plays a role as a "non-specific immune response" within the body; that the cholesterol is a response to disease and not the cause.
A study done jointly with Harvard researcher Kilmer McCully postulates how micro-organisms are surrounded and neutralized by lipoproteins (LDL cholesterol) within the blood. The invading particle, surrounded by lipoproteins, precipitates out of the blood and in healthy individuals is handled by the immune system. The theory goes that when the immune system is weak, the resulting LDL cholesterol concentrations become plaque which is unstable and prone to rupture. 
It all boils down to a "weakened immune response" leads to heart disease. This is very different from "eating saturated fats" causes heart disease. Indeed, for some groups, like the Weston A. Price foundation, mentioned above, these statements are opposite to each other.
Based on the work of Dr. Price (DDS) early last century, the foundation (which Price did not start) has some radical and controversial ideas. A bit too radical for my personal tastes. But they summarize Dr. Price's research on native/natural diets and have, I think, two interesting points. First, the macro nutrient ratios (carbs, proteins, fats) consumed by pre-industrial societies varied widely. There is no magic ratio that is the "ideal" way to eat. Secondly, no natural diet was ever found that was free of saturated fats. 
Saturated fats are actually biologically necessary. Even in vegetarian cultures, such as in India, traditional diets included saturated fats from coconuts, butter and other sources. On the opposite end of the scale, such as with the Inuit in the Arctic, meat-rich diets were so dense in nutrients and vitamins that almost no plant-based food needed to be consumed. In all these cases, not only did people intake high levels of saturated fat, but they also had relatively low rates of heart disease.
Nutritionist and W. A. Price Foundation co-founder, Mary G. Enig (PhD), contends that initial connections between saturated fats and heart disease were based on flawed studies which used hydrogenated coconut oils.  Hydrogenation is a process of chemically changing fats, usually to make them thicker. Today we know that hydrogenation leads to chemicals called trans-fats.
Natural animal fats (saturated fats) do not contain trans-fats. Cold-pressed vegetable oils such as olive oil (monounsaturated) and corn, sunflower and flax seed oils (polyunsaturated) also don't contain trans-fats. Canola oil, one of the 'heart-healthy alternatives', is a good example of a polyunsaturated oil because it contains no trans-fats. However polyunsaturated oils are unstable when heated. And heating is a part of the oil's extraction such that the canola oil you have at home can be up to 5% trans-fat, before you ever begin your cooking. 
Heating saturated fats makes them melt. But it requires temperatures higher than those used to cook, to chemically transform them. Thus, a diet rich in natural sources of saturated fats does not have many trans-fats. (Processed sources of saturated fat, such as the fats in a fast food combo meal - burger and fries - are also very high in hydrogenated trans-fats.)
It's all very confusing! Search on any of the references herein and you will see endless controversy and accusations of pseudoscience and flawed thinking from both sides. Does meat cause heart disease? Will a life of rice cakes and vegetable oil keep us healthy?
I don't know, and probably not.
In all my reading, the only constant I've seen is a series of comparisons between natural, whole foods, and processed foods. I think a lot of the research that has vilified saturated fats should actually be redone with an eye to isolating the effects of trans-fats. And I think that because of the multi-billion dollar annual investment in the lipid-hypothesis, that this research isn't going to be done. The only real conclusion I can draw is that whole, unprocessed foods, are significantly healthier for us than processed foods.
I now go over every ingredients list, when I buy food. If I see "hydrogenated" or "partially-hydrogenated" vegetable oil or E443, I put it down. I've even put down "organic, whole-wheat" bread products that were baked with thickened oil. When I cook, I have started to use natural fats like butter (grass-fed) and coconut oil (cold-pressed virgin oil). These stay chemically stable, both on the stove and in the body, and make good taste wonderful.
I believe our industrialized food manufacturing processes are harming us. I believe that choosing natural (whole, organic, home-cooked) foods is the only sane response to the insane group of theories we call "nutrition". And I believe that if we wait patiently, this situation will worsen instead of improve. As people the world-over switch to vegetable shortenings for 'heart health' more people die of heart disease.
That said, I believe that every time I buy good food I'm voting for a change. Every time I cook a meal, rather than reheat a package, I'm telling the medical and scientific and agricultural communities that people want more research. And finally, I hope, that if enough of us follow this approach, that eventually the truths will be known.
1. (1985). "Consensus conference. Lowering blood cholesterol to prevent heart disease". JAMA 253 (14): 2080–6. doi:10.1001/jama.253.14.2080. PMID 3974099
3. http://www.thincs.org/4. http://en.wikipedia.org/wiki/Uffe_Ravnskov
5. Ravnskov U. "Is atherosclerosis caused by high cholesterol?" Q J Med 2002;95:397-403.
6. Wiesel J. Die Erkrankungen arterieller Gefässe im Verlaufe akuter Infektionen. II Teil. Z Heilkunde 1906; 27:262-294.
7. Uffe Ravnskov and Kilmer S. McCully. "Review and Hypothesis: Vulnerable Plaque Formation from Obstruction of Vasa Vasorum by Homocysteinylated and Oxidized Lipoprotein Aggregates Complexed with Microbial Remnants and LDL Autoantibodies" Annals of Clinical & Laboratory Science, vol. 39, no. 1, 2009 (link)
10. http://www.truthaboutabs.com/the-canola-oil-deception.html (Note: this final reference is circular back to the work of Dr. Mary G. Enig from reference . It is included as the place I first heard these ideas.)