THE DIETARY FAT CONUNDRUM - PART 1

There is probably no subject in history that has received more print than “fat.”  First, let me say that I’m not going to talk about “fat” à la “obesity”, or “fat” à la “how to get rid of it” via exercise/diet.  What I am going to talk about is the science of dietary fat—what we think we may know about different fats and their role in the human diet.  In my opinion, the science here is not “settled,” because the weight of evidence supporting one view or another is constantly shifting.  Frankly, I’m confused. 

In fact, when it comes to fat, there is a lot to be confused about.  For one thing, the word “fat” is almost meaningless.  The only way to understand what the word means is by the context in which it is used.  For example, if someone refers to “fat” in their diet, you don’t know if they mean lard, oil, lipids, a specific fatty acid, a fatty acid supplement, or a mixture of some or all of these.  If someone refers to “fat” in their blood, you don’t know if they mean triglycerides, cholesterol, or plaque build-up.  I’d be just as happy if “fat” was eliminated from our vocabulary, as well as from our waists.

In sum, I’m more certain about the discovery of water on Mars than I am about the role of fat in the human diet.

And the subject is so complicated I think I’ll make it the topic of at least the next two blogs.  Sorry. And, I can tell you right now my objective is to wade through studies to determine if there is an emerging consensus—OK, if you read no further, I’ll tell you: there isn’t one.  At least I don’t see it. OR if there is a consensus it is very weak, so far.

For our purposes, the best way to think about fat is in terms of what it is made of:  it consists of two kinds of molecules—fatty acids and glycerol.  OK, we don’t care about glycerol (at least I think we don’t).  What we REALLY care about are fatty acids. 

What makes it confusing is that there are more than 20 different fatty acids.  And they have frightening common names:  oleic acid, palmitic acid, linoleic acid, linolenic acid, stearic acid, etc.  Further, these fatty acids can be subdivided into “saturated” fatty acids and “unsaturated” fatty acids.  Unsaturated fatty acids can be further divided into “polyunsaturated” fatty acids and “monounsaturated” fatty acids.  And unsaturated fatty acids can also be described as “cis-“ and “trans-“ fatty acids.

Saturated fat.  Trans-fat.  Polyunsaturated fats.  Peanut oil.  Olive oil.  Corn oil. Soybean oil.  Lard.  Margarine.  All of these differ from each other by the types and amounts of fatty acids they contain.

By looking at the recommendations of the American Heart Association, the World Health Organization, the American Dietetic Association, the British Heart Foundation, the World Heart Federation, the Food and Drug Administration, and others, you would assume that there is a scientific consensus regarding appropriate amounts and types of dietary fat.

I’m sticking my neck out here, but after looking at the literature I am totally convinced that this is not the case.  Let me say it in another way:  in my opinion, there is no consensus by the scientific establishment on many of the recommendations concerning the consumption of fat that we all thought were gospel.

For example, we have all heard that we should eat less “saturated” fat and eat more “polyunsaturated” and “monounsaturated” fat.  Following these recommendations, we have reduced our consumption of meat, cheese, butter, lard, pizzas, doughnuts, sausages, and cream (all high-saturated-fat foods), and increased our consumption of skim milk, nuts, chicken, fish, soybeans, margarine, and vegetables (all low-saturated-fat foods)—right? Isn’t that what we’ve been told to do for years now?

Clearly we need to take a look at the studies supporting these recommendations.   But first, let’s define what we mean by “saturated” fat, “polyunsaturated” fat, and “monounsaturated” fat.

Simply, “saturated fat” means a fat that is composed of fatty acids that don’t have any double bonds between the carbon atoms.  Simple as that.  There are five common “saturated” fatty acids (butyric acid, lauric acid, myristic acid, palmitic acid, and stearic acid).  For example, stearic acid has 18 carbon atoms, each of which is linked to another by a single chemical bond, and palmitic acid has 16 carbon atoms, also linked by single bonds.  The fat found in ground beef, for example, is composed of 15% stearic acid, 26% palmitic acid, and 4% myristic acid.  So 45% of the fat content of ground beef is saturated fat.  Therefore, the remaining 65% of the fat in ground beef is polyunsaturated and monounsaturated fat.

What is monounsaturated fat?  It is a fatty acid that has only one double bond.  There are three common monounsaturated fatty acids: palmitoleic acid (with 16 carbon atoms), and vaccinic acid and oleic acid (each with 18 carbon atoms).  Each of these fatty acids has only one place where the linkage between two carbon atoms consists of two bonds (a “double” bond).  Olive oil is a good example of a fat that is high in monounsaturates (75%).

Finally, polyunsaturated fats.  These are composed of fatty acids in which there is more than one double bond between the carbon atoms.  For example, the famous “omega 3 fatty acid” that is found in fish oil and that we’ve all been advised to ingest more of, is actually a family of polyunsaturated fatty acids, the most famous being alpha-linolenic acid, which has 18 carbon atoms and 3 double bonds.  The “omega 6 fatty acid” is another family of polyunsaturated fatty acids, of which the most famous is probably linoleic acid (not to be confused with the linolenic acid found in omega 3 above!).  Linoleic acid is 18 carbon atoms long and has 2 double bonds.

Whew.  I don’t know how anyone could keep this stuff in their heads for more than 5 seconds.  So, for now just remember that fatty acids are either saturated, monounsaturated, or polyunsaturated.

Now let’s look at the recommendation we are most familiar with:  “Thou shalt reduce the amount of saturated fat in your diet.”  What I mean is, let’s look at the scientific underpinnings of this recommendation, which is practically gospel in most nutrition circles.

Well, since the 1960’s, dozens and dozens of studies have been performed to look at saturated fats.  And, indeed, many studies show that reducing saturated fats results in a reduction in both mortality and cardiovascular disease.  However, other studies show no relationship.  So is there a consensus today?

One way at getting at the answer to this question is to look for what’s called a “meta-analysis.”  A meta-analysis is a study that groups many studies together and then performs a statistical analysis of the grouped data.  In this way you can go from an individual study of say 100 people (which I’m sure is too small to say anything definitive about dietary fat) to a single, comprehensive analysis of many grouped studies and thereby get your sample size up into the thousands.  The goal is to have a  study population that is large enough to say something definitive, that is, to do a statistical analysis that is powerful enough to identify statistically significant trends.

And for this reason I like meta-analyses.  I mean, how else can one possibly answer the question, “What do the studies say?” without looking at each of the studies individually?  A criticism of meta-analyses is that since they group many studies, they may lump sexes, races, ages, specific disease considerations, dietary interventions, and research methodologies together.  Also, different studies have different numbers of people enrolled as test subjects—so a study based on 10 people should not have the same “weight” as a study with 10,000 people.  But, some of these problems can be controlled by the scientists who are doing the meta-analysis:  They can specify that they will only look at studies that meet specific criteria.

So, let’s look at a meta-analysis of studies that looked at the saturated fat question.  I have found three recent such meta-analyses.

Meta-analysis #1*, published in 2011.  This particular meta-analysis only included studies of adults 18 years or older in randomized experiments, with or without risk of cardiovascular disease, that included both males and females (pregnant or lactating women excluded).  The authors settled on 60 studies with publication dates between 1965 and 2009, including 30 studies in North America, 26 in Europe, 3 in Australia/New Zealand, and one in the Middle East. There were approximately 70,000 total participants in the 60 studies combined.

For our purposes here, we can say that in one group of studies, saturated fat was reduced by approximately 30% of total calories.  The test subjects made up for the resulting calorie deficit by eating more carbohydrates, fruits, vegetables, and/or protein.

The authors’ conclusion?  The reduction in dietary saturated fat had no statistically discernable effect on mortality, stroke, heart attacks, “cardiovascular events,” cancer, or diabetes.

However, when polyunsaturated fats or monounsaturated fats were used in place of carbohydrates, vegetables, and fruits to bring the total calories back up to normal, there was a 14% reduction in “cardiovascular events”, but no specific reduction in strokes or heart attacks.  The term “cardiovascular event” was not further defined.

Meta-analysis #2**, published in 2010.  21 studies were included in the analysis, with each study covering 5 to 23 years, and a combined total of 347,747 subjects.  11 studies included men only, 2 studies included women only, and 8 included both men and women.  12 studies were conducted in North America, 6 in Europe, 2 in Japan, and one in Israel.

There was wide variation in dietary modification or the lack thereof—some of the studies actually modified the subjects’ diets, and others were based on surveys of the subjects’ behavior without any attempt at dietary modification.

Conclusion?  There was no evidence that reducing consumption of saturated fat was associated with a decrease in cardiovascular disease.

The authors of this meta-analysis point out that several individual studies have shown that reducing saturated fat and increasing polyunsaturated fat in the diet is beneficial to coronary heart disease, and that more benefits are seen as the amount of polyunsaturated fat increases and the amount of saturated fat decreases.  The authors’ own meta-analysis did not reach this conclusion, however.

So, there is a suggestion in both of these studies that reducing saturated fats and increasing polyunsaturated fats MAY have a beneficial effect on cardiovascular disease.

Which brings me to the next study.

Meta-analysis #3***, published in 2010.  8 studies, 13,614 participants.  The average length of the studies was 4.25 years.  In these studies, the test subjects REPLACED saturated fat with polyunsaturated fat in their diets.  On average, the “polyunsaturated” fat group got 15% of their energy from polyunsaturated fats, whereas on average the “saturated” fat group got only 5% of their energy from polyunsaturated fats.

The authors concluded that there was a 19% reduction in heart attacks or deaths due to cardiovascular events among the “polyunsaturated” fat group in comparison with the “saturated” fat group.

So, two of these three meta-analyses indicate that reducing saturated fats and increasing polyunsaturated fats may be beneficial.

Now for something controversial.  If no one responds to this, I’ll know that nobody has read this blog!  Here is the deal:  These three studies also reported on summary results for the individual studies, and SOME of the individual studies showed that THE REDUCED SATURATED-FAT DIETS WERE CORRELATED WITH AN INCREASE IN DEATHS/CARDIOVASCULAR EVENTS.  Let me say that a different way:  Some (many) of the individual studies showed that decreasing saturated fats in the diet was actually HARMFUL.

What is interesting is that none of the authors discussed this.  Is that because it would have been too controversial?  Is that because no one wants to advocate a diet high in saturated fat, when we have been told for decades that saturated fat is evil?  I do not know.

Further, an analysis was done in the second meta-analysis to test for reporting bias, and the authors concluded that there may be some.  That is, studies showing negative results may be under-reported.  In this case, a finding that decreasing your consumption of saturated fat is bad for you would be considered a negative result.

What do I think?  I don’t know for sure, but I suspect that too few subjects have been analyzed thus far and that the dietary interventions used in these studies were not detailed enough.  For example, suppose that in order to lower intake of saturated fat, you ask the test subjects to reduce their consumption of red meat.  The problem is that red meat is about 50% saturated fat and 50% monounsaturated fat.  So when you analyze the results, are you seeing the effects of reduced saturated fats or reduced monounsaturated fats?  Further, there are many different types of polyunsaturated fats—some may be “good,” and some may be “bad.”  If a test subject decreases consumption of saturated fat and increases consumption of  a “bad” polyunsaturated fat (such as, perhaps, the omega 6 fatty acids found in safflower oil), then the two may cancel each other out.  Who knows?

Do I think there is something counter-intuitive is going on here with regard to consumption of fatty acids?  There is certainly that suggestion.  Do I think you should conclude that increasing saturated fat in your diet is good for you?   No, the data does not say that, and neither am I.  Am I saying that consumption of saturated fat is neutral (neither good nor bad)?  Don’t know that either.  Do I think increasing SOME TYPES OF polyunsaturated fats may be beneficial?  Some of the data suggest that. 

And so, after looking at the conclusions reached in all these studies and struggling to read the itty-bitty fine print in those charts, am I still confused?  Yes.  Do I think you should get yearly blood tests for cholesterol, triglycerides, and all the other usual suspects?  Definitely.  Do I think you should lose weight, get more exercise, and decrease overall calories and probably carbohydrates as well?  Absolutely.  Do I have a lot of data to support these assertions?  Not yet!
_____________________
* Hooper L, Summerbell CD, Thompson R, Sills D, Roberts FG, Moore H, Smith GD (July 2011). "Reduced or modified dietary fat for preventing cardiovascular disease". The Cochrane Library (7): CD002137
**Siri-Tarino et. al. 2010. Meta-Analysis of Prospective Cohort Studies Evaluating the Association of Saturated Fat with Cardiovascular Disease. The American Journal of Clinical Nutrition 91 (3): 535–46
*** Mozaffarian D, Micha R, Wallace S (March 2010). Katan, Martijn B. ed. "Effects on Coronary Heart Disease of Increasing Polyunsaturated Fat in Place of Saturated Fat: A Systematic Review and Meta-Analysis of Randomized Controlled Trials". PLoS Medicine 7 (3): 1–10

PATENT PIRACY IN SEED CROPS

There is a very important issue pending before the Supreme Court.  It deals specifically with what most of us would think is an obscure issue, yet if the Court rules “the wrong way,” our food security, the fate of the agricultural seed industry, and the future of the biotechnology industry may all be in jeopardy.  And who knows, it may even cause a re-look at software piracy.

Here’s the big question:  As a patent owner, do you have the ability to prevent others from making your patented invention?  Now, you’d think this is a pretty obvious “yes.”  After all, that is what the patent system is for:  to give you the right to prohibit others from “making, using and selling.”

But the answer to this question also involves another very important issue:  Does the purchaser of a patented invention have the right to re-sell it, with no payment back to the patent holder?  For example, if you buy a laptop computer, which is composed of dozens if not hundreds of patented inventions, do you have the right to re-sell it? The answer, of course, is yes.  And this is the way it should be.  That is because the patent holder, say the owner of a patent on certain “chip” in your laptop, made its profit when it sold that chip to the laptop manufacturer.  This makes sense.  When the laptop manufacturer subsequently sells the computer to you, it isn’t required to give the owner of the chip patent any of the money you pay for your new laptop because the patent holder has already made its money—once.  The idea is that the owner of a patent cannot extend the “reach” of that patent beyond the first sale, and at that point, the patent holder’s rights are said to be “exhausted”.

This concept is known, logically enough, as “patent exhaustion.”

However, in the example above, no one will have the right to make MORE chips without the patent holder’s permission.

The same idea holds with copyrights.  If you buy sheet music or a CD, you can re-sell it without owing any money to the author (or whoever owns the copyright).  All is good—we live in a rational universe and this makes sense.  On the other hand, we all know that if you buy a CD, that doesn’t give you the right to copy it.  And buying sheet music doesn’t give you the right to reprint it.  That is “piracy.”  The copyright owner is the only one who can reproduce the copyrighted material or grant permission for others to do so.

Same with patented inventions.  The patent owner has the right to prevent everybody else on either from manufacturing his invention.

Now to the case in point.  If you are the owner of a patented gene that you have inserted into the DNA of a plant, you have the right to sell seed from that plant to other people for any purpose.  And if a farmer plants that seed and it makes new seeds containing your patented gene, he can sell those seeds (as grain for food) to make money on his soybean, or corn, or rice, or whatever crop has the patented gene.  The grain then enters the food chain and is bought and sold throughout the world without payment back to you as the original owner of that gene.  This, of course, is the way many companies such as Monsanto, DuPont, Syngenta, and Bayer, to name just a few, profit from their research and inventive activity:  they sell genetically-modified seeds to growers for planting.  But they don’t get any additional money when the resulting crops are eventually sold (and resold) for consumption by animals or humans.  This all makes sense, of course.

Is that like being able to re-sell the laptop containing a patented chip?  Sure it is.  You have the right to re-sell used laptops on eBay even if they contain chips patented by somebody else, and you will owe no money back to the original patent owner.  And likewise, the farmer has the right to sell patented seeds as food, and everyone from commodity brokers to the local Co-op has the right to resell those seeds for the same purpose.  But does the farmer who buys patented seed have the right to plant those seeds, collect new seeds from the resulting crops, and then sell those seeds to somebody else for planting?  That would make NO sense.  We already know that you can’t copy a company’s computer chip, and planting seeds is actually like making an exact replica of the original.  I think you’d all agree with that . . . . 

And so, up until now, courts have ruled that a patent owner can prevent farmers from collecting “excess” seeds they have produced and then re-planting or selling them to other people for planting.  Farmers are permitted, of course, to sell seed (grain) for animal feed, human consumption, etc. because in that case the seed will eventually be eaten, not planted.  In other words, when patented seed is consumed, it is not being used as a “factory” to make more seeds, which would infringe the patent owner’s exclusive right to keep others from manufacturing his patented invention.

The Bowman v. Monsanto case before the Supreme Court involves an Indiana farmer who bought Monsanto’s RoundUp Ready soybeans, which contain a gene that makes the crops grown from these seeds resistant to Monsanto’s RoundUp herbicide.  Fine so far.  Farmer Bowman then harvested these seeds and sold them to a grain elevator in the usual way.  Still fine, because seeds sold to grain elevators are for consumption.  Then he bought seeds from the elevator because he could get them at a much lower price than he would have paid for RoundUp Ready seeds if he bought them directly from Monsanto.  Since more than 95% of all soybean seeds planted in the United States are RoundUp Ready, he was pretty certain that he would get largely RoundUp Ready soybeans.  The farmer was still okay at this point.  But then he planted those seeds, SPRAYED them with RoundUp (thus selecting, or “enriching” his yield of the patented seeds), harvested the excess seeds, and replanted them, thus avoiding the cost of buying new seeds from Monsanto.  He did this for 8 years.  This last bit was not okay.   Monsanto sued him in federal court and won an $87,000 judgment.  Seems logical to me.

Now, this was a pretty cute move by farmer Bowman.  Hey, what a great way to get your very own supply of high-technology seeds—essentially for free!  So when he was finally caught, the U.S. District Court found him guilty of patent infringement.  Good call.  The U.S. Court of Appeals upheld the decision of the lower court, and now the case has found its way to  the Supreme Court as Bowman v. Monsanto (Case # 11-796).  Oral arguments were heard this month (February, 2013) and a decision is expected by June.

Bowman is using as a defense the concept of “patent exhaustion,” described above.  His position is that once he purchases Monsanto’s patented seed, he can do whatever he wants with it.  In this case, plant and re-plant it forever—and avoid paying seed costs. 

Now, this issue also raises the concept of “farmers rights.”  You are going to have to bear with me here, but basically many farmers in the United States generally side with Bowman because of the Plant Variety Protection Act (PVPA).  The PVPA provides an alternative form of intellectual property protection that is available to developers of new seed-bearing plant varieties.  Thus a plant breeder can obtain a Plant Variety Certificate (PVC) under the PVPA on a new soybean variety that provides patent-like protection for 20 years.  And under the PVPA, there is an “exception” that allows farmers to use PVC-protected seed for their own seed planting needs.   This is known as the “farmers exemption.”

So in other words, if Monsanto had protected its RoundUp Ready soybeans ONLY with a Plant Variety Certificate, then Bowman would have been within his rights to save seed for replanting.  But Monsanto did NOT use the PVC form of protection; it used the patent system, which is a “tougher” form of protection that does NOT have a farmers exemption.

Not, that is, unless you are trying, like Bowman, to argue that a farmer’s exemption should exist for patented varieties through the concept of “patent exhaustion.”

Whew.  I hope you’re still with me.

So, to repeat myself, the decision in this case by the Supreme Court will be extremely important.  A decision in Bowman’s favor would have the unwanted effects of:
(1) substantially reducing the protection offered by patents on OTHER types of inventions (besides plants) that rely on self-replication—basically anything that has the ability to “remake” itself, including genetically modified materials such as cell lines, bacteria, and viruses (as well as the products of a NEW industry that is only now developing in the area of “synthetic biology”, the topic of another blog someday!), and
(2) totally eviscerating the seed industry by taking away any incentive for companies to invent new varieties of plants that reproduce by self-pollination, such as soybeans, peanuts, wheat, rice, and barley.  (Note that I have excluded corn, since corn is planted by farmers as hybrid corn; if the farmer re-planted hybrid corn it would degenerate into many different genotypes/varieties.)

For decades, there has been a desire in the United States to limit the ability of companies to make money from their innovations (e.g., plant varieties).  Apparently, many people think that if a company makes an invention, that new technology should immediately become available to the public with no restrictions—so essentially you and I should get it for free.

Further, there is a time-honored activity in the United States known as “brown bagging”, which is the practice of harvesting seeds that are protected by Plant Variety Certificates and/or patents, putting the seeds into “brown bags,” and selling them to the neighbors.  (While the “farmer’s exemption” permits growers to save PVC-protected seeds for re-planting, it does not permit them to sell those saved seeds to other growers.)  This practice still goes on, and in fact new PVC-protected wheat varieties developed at Oklahoma State University are subject to occasional “brown bagging.”  As you would expect, when OSU learns of such illegal practices, we come down on them hard.  As we should.

You just can’t make copies of protected “materials”—not copyrighted CDs and not patented seeds.

You’re already familiar with software piracy.  Now you know about “seed piracy” too.  Same idea.

THE ROLE OF PATENTS IN THE KNOWLEDGE ECONOMY: APPLE V. SAMSUNG

The U.S. patent system recognizes three types of patents: utility patents (most common), design patents, and plant patents.  The first, utility patents, covers inventions that are unique, non-obvious, and useful.  The second covers, well, the design of an object.  The third, as the name implies, covers plants (specifically, most vegetatively propagated plants).

The recent Samsung v. Apple lawsuit is based on four design patents held by Apple: USD604305, USD593087, USD618677, and USD504889.  Please look them up.  They are very easy to understand because the first three LOOK like the iPhone and the fourth LOOKS like the iPad.  Apparently the jury thought that they also look like the Samsung Galaxy S and Galaxy SII (phones) and the Galaxy Tab 10 (a tablet) because the suit resulted in a win for Apple of over $1 billion for infringement of its patents.

The Samsung v. Apple case also involves three utility patents held by Apple:  US 7,469,381; US 7,864,163; and US 7,844,915.  Look these up too.  Among other things, these patents cover various functions that we are familiar with, such as scrolling, pinch to zoom, and the “bounce back” to indicate that we have scrolled beyond the edge of a page.  In its effort to get these Apple patents invalidated, Samsung argued that they were predated by the multi-user DiamondTouch(TM) tabletop developed by Mitsubishi in 2001, which had an early version of “pinch to zoom”.   They also maintained that Roger Fidler’s vision for a digital newspaper tablet way back in 1994 preceded at least one of Apple’s patents.  Ultimately Samsung lost because the jury was not convinced that these other innovations were enough like Apple’s inventions to justify the invalidation of Apple’s patents.  The jury also failed to find that Apple had infringed three Samsung patents covering emailing pictures, multi-tasking while playing music on the phone, and switching between pictures in a picture gallery and the camera. 

Clearly Apple’s United States patents give it the right to keep other companies from “making, using, and selling” infringing devices in the United States.  But what about other countries?  These patents have also been filed in many places around the world, and in those countries that have allowed the patents to issue, Apple will have essentially the same rights that it has in the United States.  It is one of these foreign patents covering the “overscroll bounce” that was involved in Apple’s German lawsuit against Motorola Mobility, a Google subsidiary.  Apparently a judge in Munich agreed with the jury in Silicon Valley, where the Samsung case was tried, because the Motorola case was decided in Apple’s favor on September 14.  As a result, Google’s Motorola unit faces the possibility that it will be forced to recall its Android tablets and smartphones in Germany.  However, Apple will have to request such a recall, and Google is expected to appeal.  Moreover, Google may just eliminate the “bounce” function and replace it with its own “glow effect” to indicate that the user has reached the end of a page.  There’s more than one way to skin a cat.

As a result of the proliferation of lawsuits surrounding phone and tablet technology, a lot of people are saying that the patent system is “broken.”  In fact, it is doing exactly what it was intended to do: protecting innovation.  These digital devices are complicated and each one of them incorporates many different inventions; it is reasonable to expect disputes on “who invented what when” as patent owners like Apple and Samsung seek to enforce their patents on those inventions.  It goes like this:   If you think you have an idea for a better-looking mousetrap, maybe you can get a design patent on it.  You may think such a patent is trivial.  Doesn’t matter.  If the public buys that mousetrap because they like how it looks, well, your design patent gives you the right to keep another company from capitalizing on your success by selling a mousetrap that looks a lot like yours.   So you file a lawsuit against that company and ask the court to enforce your patent.  Shouldn’t you be one who profits from that design because YOU are the one who came up with it?  The signers of the U.S. Constitution thought so. 

One thing seems clear to me: these cases will spur MORE innovation in both design and functionality, as inventors try to “get around” Apple’s patents.  Isn’t that a good thing?  Sure, some products may become unavailable, and some companies may go out of business.  But there will be new products and maybe even new companies to take their place.

Welcome to the world of competition and the value of innovative ideas.  The world has never before seen a time when mere “ideas” had such value.  It is no accident that highly innovative companies such as Google and Apple are among the most valuable in the world.

SIFTING AND WINNOWING: ACADEMIC TENURE AND COMMERCIALIZATION ACTIVITIES

The tenure concept at American universities dates at least back to the 1870’s when  the tenure system was developed to ensure employment protection when a faculty member engages in research or teaching on topics that may be controversial.

An early pivotal case involved Richard Ely, a professor at the University of Wisconsin who was advocating labor strikes and labor reform.  In 1894, the state legislature and various business interests tried, unsuccessfully, to pressure the university to fire him.  One of the results of that case was what must be the most elegant statement ever penned about the importance of academic freedom to a university.  It is immortalized on a plaque at the University of Wisconsin, Madison:

"In all lines of academic investigation it is of the utmost importance that the investigator should be absolutely free to follow the indications of truth wherever they may lead.  Whatever may be the limitations which trammel inquiry elsewhere, we believe the great state University of Wisconsin should ever encourage that continual and fearless sifting and winnowing by which alone the truth can be found."

And so the tenure concept developed, and by 1910, 22 universities had hired faculty with a presumption of permanence. 

Today most, if not all, universities have a tenure system whose details are governed by each individual university’s policies and procedures.  General similarities exist among all such policies—in order to get tenure, junior faculty must show competence in research, publishing, teaching, ability to get grants, etc.   However, the entire concept of tenure is still being debated, pro and con.  Much of this debate involves a related concept: “performance” evaluation.  That is, how does a university decide whether or not a faculty member is “doing a good job”?  This difficult question is answered by various universities in different ways, and with the increasing focus on technology transfer, a new criterion has emerged within the past several years.

In 2006 the Texas A&M System Board of Regents voted to “consider faculty members’ commercialization success in tenure applications.”  This created quite a stir; a 2011¹ survey shows that 75% of universities do NOT use commercialization as a tenure/promotion criterion.  However, of those that do include commercialization activities, most of them developed such policies before 2006.  So, some universities have been on this track for quite some time; they are “early adopters.”

Universities vary as to what falls under the umbrella of “commercialization activities and economic development.” Such metrics include patents filed, patents issued, and royalties generated.  Others may include new company startup activities and corporate research funding.

Based on the 2011 survey, the majority of universities that consider “commercialization activities” as part of tenure and promotion have research budgets that are mid-sized to small (less than $147 million).  The obvious conclusion to be reached is that these universities value faculty who augment their budgets with additional revenue. 

It seems to me, however, that no matter the size of the university, credit should be given for commercialization efforts on the part of their faculty.  After all, don’t the taxpayers who fund state-supported schools expect faculty to do research that benefits society?  And isn’t “commercial impact,” along with other conventional measures, a good measure of benefit to society?


¹Ashley J. Stevens, Ginger A. Johnson, and Paul R. Sanberg. 2011. The Role of Patents and Commercialization in the Tenure and Promotion Process. Technology and Innovation, Vol. 13, pp. 241-248.

33 RPM RECORDS TO DNA MEMORY STORAGE

For many of us still on the stage, our earliest exposure to “memory storage” had to do with the number of songs we could get on a “45” or “33” rpm record.  I never bought a “45” because they only had one song per side.  However, each “33” had about 5 songs per side (around 15 minutes), and I always thought that was a better deal.  And so it was through the age of cassette tapes in the 1970s, CD’s in the 1980s, and on to wherever we are now. 

My first brush with computer memory storage was the 80-column punch cards used in the 1970s.  Hundreds, no, thousands of punch cards.  We used to haul around boxes of those things with 2000 cards per box.  Those I understood.  And it turns out, the basic function of the punch card was the same as that of the hard disk in your computer:  to encode either a “zero” or a “1” in various combinations.  Each “1” or “0” was (and is) called a “bit”.  A string of 1s and 0s eight bits long comprises a “byte”, which represents one character, such as a letter or a number.   (I find it easier to think of a byte as “word” written in an alphabet of only 0s and 1s, but my physicist son has tactfully pointed out that that is just not correct.).  A typical book of 500 pages is about one million bytes—a “megabyte”.  So is a 4-megapixel JPEG image.  Or one minute of 128 kbit/sec MP3 compressed music.  You get the idea.

With increased information being stored, our vocabulary has increased from megabytes to “gigabytes,” each of which is 1000 megabytes (a billion bytes).  The next multiple of a thousand is a “terabyte”, and so on.  A “yottabyte” has 24 zeros.  I don’t even want to know how many punch cards that would be.  Fortunately, bytes now are encoded magnetically (credit card), optically (CD), or on a semiconductor (computer, iPod). 

It is interesting to take a peak over the horizon towards new computer storage media.  It seems that the likeliest future contenders will utilize quantum mechanics or DNA.  Quantum computing allocates 0s and 1s to the spin direction of individual electrons, atoms, photons, or molecules.  They spin one way and they are a 0.  Another way they are a 1.  And, for another new vocabulary word, if it is both a 0 and 1, it is a “qubit”.  Don’t ask me how an electron can simultaneously have two different spins.  I don’t think physicists know either—just one of the spooky things that have emerged from small particle physics.  BUT, they have actually made elements of a quantum computer, and Australians claim that quantum computing will be here in 5-10 years.

Now for the good stuff--DNA computing!  DNA is composed of 4 bases—A, T, G, and C.  It is the basic genetic component for all of life—bacteria to humans.  The sequence of the bases forms a genetic code.  What researchers have done is to assign the number 0 to A or C, and 1 to T or G.   So the sequence AAG is 001.  So is CCG.  The letter “F”, for example, would receive a unique string of eight bases, and comprise one byte of information.  In order that the stored information can be retrieved, a string of bases in the nature of a “bar code” is added at the start of the sequence to indicate where in the text that specific letter shows up.

In a paper published in August, Harvard researchers report that they used this technique, plus the most modern methods of DNA sequencing, replication, and reading, to encode a 53,000-word book with 11 images (5.2 megabits) onto 55,000 DNA strands.  They were subsequently able to “read” these back and voila—recreate the book.

You might well ask what is the point of going through all this effort to devise a method that uses DNA to accomplish something that could be done easily on your laptop?  Mostly it has to do with storage capability:  70 billion DNA copies of our 500-page book would fit onto an area the size of your fingernail.  The Harvard researchers estimate that every bit of human-created digital information currently in existence could be stored in only 4 grams of DNA, a feat made possible, in part, by the fact that this is three-dimensional storage.  Think DNA in a beaker, as opposed to molecules on the flat discs of your hard drive.  Another advantage is that DNA is quite stable—so stable in fact that researchers have been able to isolate intact DNA from extinct mammoths.  And finally, DNA can be copied with high reliability, as is going on within your cells this very moment.

So how does this compare with quantum computing?  The expectation, as I understand it, is that quantum computing will be faster, but DNA information storage will be hugely greater.  And what about a quantum computer linked with a DNA storage system?  Wow!  I hope I live that long. 

And how does DNA memory compare to other sorts of storage such as flash drives and CDs?  DNA memory>quantum holography>bacteria>flash memory>DVDs, with DNA memory being 1000 times greater per unit of volume than quantum memory and 100 billion times greater than a CD. 

It turns out that, of course, patent applications have been filed in the area of DNA computing.  Not many, but there are a few.  Since patents only last 20 years from date of filing, an application filed today will be worthless unless a commercial product can be developed in the next 20 years.  One may ask how many sales of DNA storage media could be made—that is, could this become a consumer product? I doubt it.  One sale to Google to store all information known to mankind?  Maybe.  I’m not sure I’d be willing to spend $50,000 or so to get a patent in this field. 

But then again, in the early 1990’s, I couldn’t see the need for a 20 MB hard drive on an Apple SE either.

ANCIENT DNA AND US

Reports comparing our DNA with that of our extinct ancestors are coming in so fast and are so momentous that it is just exhausting trying to keep up!   Rapid advances in DNA technology have resulted in discoveries that were thought to have improbable just ten years ago.  It seems every month brings a new announcement regarding human evolution that is so persuasive that many long-festering debates are now essentially over.   (Well, as “over” as they ever are in science, which means the next five years will probably overturn what we think we know today.)

When the first reports of soft tissue being isolated from a 65-million-year-old Tyrannosaurus rex thigh bone hit the press in 2005, the world’s collective jaw dropped.  The researchers described finding blood vessels and collagen (the main protein in connective tissue) in otherwise fossilized bone.  Who would have ever thought such a thing was possible?  Then two years later, an analysis of the amino acid sequence of the collagen protein indicated that, when compared to modern animals, it was most closely related to chickens, thus providing very nice independent confirmation that birds are direct descendants of dinosaurs, a theory that was previously based solely on skeletal comparisons.  It is so satisfying when independent discoveries reinforce each other—it just doesn’t get any better than that!

While we have had pretty good luck in finding these very ancient proteins, isolating ancient DNA has been much more difficult because of its susceptibility to degradation from exposure to the elements, particularly moisture and heat.   Because it is so very precise, ancient DNA is the Holy Grail of on-going efforts to work out the evolutionary connections between modern humans and our ancestors.  After all, if DNA can be used as conclusive proof of genetic identity in forensic science why wouldn’t it be just as powerful for establishing evolutionary relationships?

So far the oldest DNA has been found in remains of modern human ancestors. In 1997 the first DNA extractions were made from a Neanderthal skeleton estimated to be between 30,000 and 100,000 years old, based on classical fossil dating techniques.  Then in 2010, a complete DNA analysis was done on the entire Neanderthal genome (that is, all of its DNA), and the results were compared to the human genome.   Pretty impressive, but not so impressive as the conclusion:  that 1-4% of European DNA may have been inherited from the Neanderthals.

In 2011 the same researchers analyzed DNA extractions from a 50,000-year-old skeleton from Siberia.  Holy cow—turns out SHE is distinct enough to be placed in a new category separate from Neanderthal—Denisovan.   So now we have three major contemporaneous humanoid groups:  Neanderthals, Denisovans, and humans, all genetically very similar.

Then in 2012, it was reported that researchers had compared DNA from the Denisovan girl to DNA from modern humans and found 111,812 single-nucleotide differences.  That sounds like a lot, but since the human genome has six billion nucleotides, it is actually pretty small (a difference of a little more than a thousandth of one percent).   The Denisovan genome is so complete that researchers have been able to determine the color of the individual’s eyes, hair, and skin.   More importantly, they have detected differences in various genes associated with speech disorders, disease, and the wiring of the nervous system.   Think about it—this means that in the not-so-distant future scientists may be able to tell exactly what genetic changes would be necessary to convert a Denisovan or Neanderthal into a modern human—or the reverse!

That brings up another really interesting question, which is how much humans have in common with chimpanzees, our closest non-human “relatives”.  It turns out that chimp DNA differs from human DNA, on average, by only about 90 million nucleotides (1.5%).  You could say that chimpanzees are 98.5% human, but they might not take it as a compliment since by these same measures, a banana is about 60% human.

Another question, and one that has been at the root of the human evolution debates, is how long ago did humans and chimps diverge?  Well, another paper published just this August pretty much nails it.   First of all, based only on fossil evidence from the 400 or so skeletons that have been found so far, it has been estimated that Neanderthals lived from about 800,000 to 40,000 years ago.  The same fossil evidence has placed the divergence between chimps and humans at three to five million years ago. 

The problem is that fossil dating is uncertain.  Fossils are found in rocks after all—they ARE rocks.  Rocks move.  And erode.  And get contaminated.  So in spite of the use of elaborate techniques based on elemental changes that are known to have occurred in rock over time, the dating of fossils remains subject to question.  This has always cast doubt on the conclusions reached by anthropologists concerning the timeline for human/chimp divergence.  So what we really need is another way to get at the answer to this question that avoids the problems associated with fossil dating.

It turns out that DNA changes over time at a rate that can be used to BACK CALCULATE how old skeletons are.  How?  By using the rate of change from one generation to the next.  This means that known rates of change in DNA can be used to determine the age of Neanderthal and Denisovan skeletons as well as to estimate the time elapsed since the divergence of humans and chimps.   The way this is done is by comparing the differences in DNA between parents and offspring.  If you know how long a single generation lasts (25-30 years in both chimps and humans), you can calculate the spontaneous mutation rate (number of changes in nucleotides/year).  And that is all you need.

An August 2012 paper reported that the application of the known mutation rate to the analysis of chimp DNA indicates that divergence between chimps and humans occurred 7-8 million years ago.  These DNA-based findings place the split a bit earlier than the fossil-derived dates geologists and anthropologists have been giving us for years, but not egregiously so.  The same kind of calculations for Neanderthal DNA shows a human split between the two of about 400,000 to 800,000 years ago—within the range that anthropologists have found using fossil data.

And so we have two COMPLETELY different methods of estimating the timeframe for human evolution, and they are very concordant considering the vast lengths of time involved.  No longer can one dispute the estimates by arguments against “old fossils” and their presumed inaccuracy in dating.  (Well, I guess you could, but that argument is now very much weakened, at least in my mind.)

There are many more questions remaining to be answered.  First, it is important to stress that even though there is a smooth continuum in terms of genetic differences between Neanderthals and humans, and between Denisovans and humans, that does not mean humans descended from these ancient “cousins.”  In fact, the skeletal information says they did not. Neanderthals and humans probably shared a common ancestor—perhaps the well-known Homo erectus, who lived from about 1.8 million to 300,000 years ago.    Exactly where Homo erectus and the far older Homo habilis (2.3 million to 1.4 million years ago) fit into this ever-more-branching and complicated picture remains to be seen.  Then there is the genus Australopithecus, which may have given rise to the genus Homo, and lived 4 million to 2 million years ago.  Australopithecus itself has 3-4 species, depending on one’s taxonomic orientation.  Closely related to Australopithecus is the genus Paranthropus, who appeared on the scene 2.7 million years ago.  And then there is Ardipithecus, which may have predated the split between chimpanzees and humans.

And so we have a virtual bestiary of bi-pedal ancestors, a thorny bush of complex relationships, many competing to be Homo’s ancestor.   But you can rest assured that if researchers are able to isolate proteins from a 65-million-year-old T. rex and DNA from 100,000-year-old skeletons, there are scientists out there somewhere who are trying to isolate proteins and possibly even DNA from Homo erectus, and maybe even from Australopithecus and Paranthropus fossils.  And maybe proteins will be found to be just as diagnostic for fossil age as DNA is turning out to be.

These complex taxonomic and evolutionary relationships will be sorted out in time.  As the cost of molecular investigation continues to fall and more and more people learn the laboratory techniques involved, the Homo family tree will probably be simplified.  The time is ripe for collaborations between anthropologists and geneticists to answer questions that have been around for 150 years.

But, as with all science, there will be huge surprises.  New skeletons will be found and theories will be overturned.  But with enough research funding, good science moves inexorably forward.

THE SPACE STATION AND NASA SPIN-OFFS

Recently I was reading an article about the success of a for-profit company called SpaceX in linking with the International Space Station, and I started wondering—why do we have a space station, and who cares?  Well, actually, I care, but it occurred to me that a lot of people probably don’t even know why it’s there or what it is doing.  So I started writing a blog post about the space station, which in turn made me curious about NASA outputs—that is, what have we gotten for our investment in the space program?

I guess I knew that NASA didn’t invent Teflon (DuPont, 1938).  But I was pretty amazed to learn that they didn’t invent Tang (General Foods, 1957) or Velcro (the Swiss,1940s) either.  Nor did they invent bar codes, quartz clocks, or smoke detectors.  So much for urban myths.

But if John Glenn did not invent Tang, what spinoffs have emerged from the space program? 

Well, first, I guess we need to look at the input.   That is, what has the space program cost the U.S.?   So, adjusted for inflation, here are the numbers in 2007 dollars:  During the first year,1958, it cost $488 million.  The next year the annual cost reached $2 billion, and by 1962 it was up to $12 billion.  Costs doubled to $24 billion in 1963, and from 1963 to 1970 the budget was always above $18 billion per year. Since 1970 the budget has been fairly stable, hovering somewhere between $11 billion and $17 billion per year, with .the grand total in 2007 dollars being somewhere in the neighborhood of $790 billion.   Another way to look at the numbers is as a percentage of the U.S. federal budget.   At its peak in the 1960s, the space program accounted for 4% of the federal budget.  Now it is only 0.5%.

Now for the outputs—that is, what have we gotten out of the space program?  Well, I’m not going to wax eloquent about aesthetics—though NASA’s photos ARE pretty cool.   I’m especially not going to mention the famous Earthrise photo taken in 1968 by William Anders during Apollo 8, which gave us the first glimpse of our home as a blue ball hanging in the blackness of space and had a significant impact on our appreciation of the planet.  Nor am I going to mention the thousands of children who became engineers or scientists as a result of the space program, though one survey said 80% of such folks were motivated by the walk on the moon.  (I was not—when we landed on the moon I was knee deep in a swamp looking for raccoon tracks, intent on becoming a trapper.)  And finally, I am not going to mention our increased understanding of the Universe.

So what were the outputs?  First, most of that $790 billion investment was spent here in the U.S.  We hired people, lots of people—400,000 NASA employees, scientists, and contractors from 1964 to 1967 alone.  They in turn bought houses and improved school systems.  An independent study showed that from 1958 to 1969 $25 billion (1958 dollars) were spent on space research and development, and returned  an estimated $51 billion to the U.S. GDP.  So for every $1 spent, economic output increased by $2.  A 1976 study concluded that for every $1 billion spent on manufacturing, manufacturing output increased  0.1 percent, and in 1976 dollars that would be $153 Billion.  That alone exceeds the total space program budget up to that time.  Many studies have shown that research and development has positive economic impacts down the road, and there is no reason to believe NASA’s R&D would be any different.

But what about more tangible outputs?

There are lots and lots of such outputs.  Products we all recognize and for which NASA deserves all or at least part of the credit include:  light emitting diodes (LEDs), scratch resistant lenses, grooves in concrete to reduce skidding, radial tires, de-icing systems for airplanes, corrosion detection systems, video enhancement, “memory foam” now found in everything from pillows to horse back saddles and prostheses, fire fighting equipment, fire-resistant reinforcement for such things as buildings and aircraft (too bad the Twin Towers didn’t have this), freeze dried food, the “Dustbuster”, enriched baby food, solar energy panels, thousands of computer programs including software for designing cars and amusement park rides, mine safety. . . not to mention the first weather satellite technology.  Oh, and the Speedo LZR Racer swimsuit, worn by Michael Phelps at the 2008 Summer Olympics.   And another 1,600 products/systems.

For a very interesting look at the kinds of patents NASA owns (meaning that the underlying research was conducted by NASA or by a contractor that was funded by NASA), see their wonderful website showing what is available: http://technology.nasa.gov/.  The list of inventions, all of which are succinctly described in easy-to-understand abstracts, covers everything from prosthetics to corrosion prevention.  And in case you would like to have rights to any of these technologies, make your pitch to the contacts listed on the website.  Best of luck!

Altogether, 6,393 patents are owned by NASA, of which 928 are active, meaning they have not expired (patents currently last 20 years from filing).  An additional 1,241 patents were funded by NASA but are owned by somebody else.  So if they have invested $790 billion and have produced 7,634 patents, it takes $103 million to generate one patent.  To put that in perspective, at U.S. universities it takes about $3 million in research funding to generate one patent.   By this measure, I guess you could say NASA is 34 times less efficient than U.S. universities at producing patents.  Shame on them! Yea, sure.  That is ridiculous—NASA does a lot more than produce patents. 

If you want proof, just look at Earthrise.

And I guess I didn’t say much about the Space Station.  Subject for later.