Wednesday, May 25, 2011

The insecure platform of science

In today's New Scientist are a series of remarkable articles on things that scientists have got wrong. I have quoted verbatim from the one about genes, but there are eight others taking in the periodic table, the classification of vertebrates, nuclear fission, hydrogen bonds, the limits of microscope optics, the number of separate species in the world, magnetism, and Einsteinian physics.

What defines life's building blocks? It depends who you ask, says Michael Le Page

As Gregor Mendel showed in painstaking experiments on peas in the 19th century, many traits of living things are all or nothing. Seeds are either green or yellow, round or wrinkled, and so on. This led to the idea that an organism's characteristics are determined by discrete “particles” passed from one generation to the next: genes.

But what is a gene? This question seemed to be settled with the discovery of the function of DNA in the 1950s. A gene, biologists agreed, was a DNA sequence that encoded the instructions for making a protein, the molecules that do all the work in living things.

Half a century on, such harmony has vanished. We now know that single “gene” can consist of dozens of distinct DNA segments that can be combined to make thousands of different proteins; that overlapping DNA sequences can encode quite distinct proteins; and that a few proteins are encoded by combining pieces of what were regarded as separate genes.

Even more confusingly, we are discovering ever more DNA sequences that are not blueprints for making proteins, but instead code for RNA molecules that carry out various functions directly. “If you open the door to RNA, it gets much more complicated,” says Mark Gerstein, a bioinformatics researcher at Yale University.

Reverting to an updated version of the original idea, and defining a gene simply as a DNA segment that affects the characteristics of offspring – by whatever means – doesn't help. That's because it would mean the inclusion not just of protein or RNA-encoding DNA segments, but also a myriad of regulatory DNA sequences that switch those segments' activity on or off.

These days, then, what a gene is depends on who you ask. Gerstein has suggested it be defined, in simplified terms, as a union of sequences that encodes one or more “functional products”. But he readily admits this is a fudge. “What is function?” he asks. “What does it mean?” A gene that is important for survival in one species may have become redundant in a closely related strain, for instance, even though the sequence is identical. Does that make it a gene in one species and not in the other?

It seems that unless you are an expert in a particular field you are operating in science with an enormous fudge factor. Science is fluid. There is no truth, just a succession of theories. When the facts change I change my mind, said Maynard Keynes. It seems he wasn't the only one.


Burke said...

"There is no truth, just a succession of theories."

You must realize, Doc, that this is a flat contradiction and absolutely wrong. It is supposedly a truth itself and, therefore, it contradicts itself. But more interestingly, if one accepts that the foundation of knowledge is man's senses and that all his other knowledge is built upon that, then our ONLY errors are at the higher, conceptual level. And these beliefs can be verified or refuted by observation.

Descartes claimed that every absolute "truth" that he had thought he had found turned out to be wrong.

But how did he determine that his belief was wrong except by determining what was true?

Those who accept the view you espouse here are wrongly describing the growth of knowledge as a succession of setbacks.

The fact that men are not omniscient does not mean that they know nothing.

Terry Hamblin said...

Yes, I expressed myself badly. There is an absolute truth, it's just that our knowledge of scientific truth falls short of it. Scientific truth is contingent on the information available.

Burke said...

There was a time when people thought the world was (relatively) flat. When the looked around, they saw the terrain going up, but coming down again, etc. And they assumed erroneously that it went on and on that way. But then they noticed that the masts of ships disappeared before the hulls when sailing away and some other things. And they concluded that the Earth was round. They have since learned that it is not exactly round, but mostly so.

Is this not a certain scientific truth?

Was it established *only* by disproving erroneous scientific theories?

Terry Hamblin said...

It's a myth that people ever thought the world was flat.

Burke said...

Never heard that before.

Terry Hamblin said...

Yes, there was an Ancient Greek (c 800 BC) who believed it but it has long been known that the earth is approximately spherical - certainly for over 2000 years, probably more like 3000. Navigation by sea makes it very plain. This story of flat-earthists is just a stick to beat anyone who doesn't follow the latest scientific fashions.

Since science has been formulized and formalized, the currectly accepted truth is an hypothesis of theory. It is only as good as an approximation of the truth according to the information available. The scientific method acts by trying to disprove the current theory and failure to do so strengthens the regard in which is held. Unfortunately some scientists think their duty is to try and bolster the current theories rather than refute them. I cite the East Anglian climatologists as an example.

Terry Hamblin said...

Sorry should be hypothesis or theory.

Burke said...

But here is the rub:

"The scientific method acts by trying to disprove the current theory . . . ."

Disprove how?

Do we determine the composition of the moon by first disproving that it is made of blue cheese and then continue disproving that it is made of the countless other materials that exist?

How do you disprove that A is B? Only by being able to
identify B. Right? But how do we identify B? By establishing that it is not C? And on and on, etc.-- in an endless regression.

Where do we get our theories and hypotheticals in the first

From observation, from our senses.

Everything we know is built on a foundation provided by our senses. It's a growth process.

And, since, our senses are physical entities responding to physical stimuli, they cannot give us anything but the facts.

Which means that, contrary to popular belief, we are capable of certainty and truth.

All our errors are just assumptions we make at the conceptual level.

Terry Hamblin said...

It's complicated. You experiment. If A is true then in this experiment B could not be C. If B is C then A is not true. The more frequently B is not C then the more likely A is true. Util the day that technology increases and allows you to imagine a do-able experiment that tests the theory to destruction.

Observation is the first stage in hypothesis generation, but imagination plays a part.

I quite accept that we are capable of certainty and truth, but such truth is usually incomplete. There is almost always a more complete truth to know. Newtonian physics is true, but an incomplete truth. Under exceptional circumstances they do not apply and Einsteinian variations are necessary. Even Einstein is probably not a complete truth.

Burke said...

"Newtonian physics is true, but an incomplete truth. Under exceptional circumstances they do not apply and Einsteinian variations are necessary. Even Einstein is probably not a complete truth."

I understand your point here, but I think that the notion of there being an "incomplete truth " is not quite the way it should be expressed.

The fact that we can't see the back side of the moon doesn't mean that the knowledge we have regarding the front side is incomplete. Similarly, Newton's determination that force equals mass times accelleration correctly described what he perceived. Einstein learned later that mass increases as an object approaches the speed of light, but Newton had never really observed or attempted to describe such action.

Concept formation and descriptions of reality contained in groups of concepts (principles) are man's way of condensing the vast amount of sensory data we receive into things he can mentally grasp and retain.

Cognition is an act of identification. If Newton's law does not describe the action of objects at great speeds, that doesn't mean that it's wrong. It just means that different circumstances require different laws.

In principle, no different than the moon example.

Terry Hamblin said...

Yes, that is a satisfactory way of putting it. I would not like to be thought to be giving support to the post-modernists.