Darwinian Evolution Considered As a Phase

LucidBeast tips a mind-bending report at New Scientist on the latest paradigm-breaking work of Carl Woese, one of whose earlier discoveries was the third branch of life on Earth, the Archaea. Woese and physicist Nigel Goldenfeld argue that, even in its sophisticated modern form, Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth. Woese and Goldenfeld believe that horizontal evolution led to the rise of the genetic code itself. "At the root of this idea is overwhelming recent evidence for horizontal gene transfer — in which organisms acquire genetic material 'horizontally' from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself."

Comments

Re:Here's A Tip, Folks

[MightyMartian]

I'm not trying to take away anyone's "sense of wonder". I'm saying that horizontal gene transfer is one known way in which variation can occur. Remember, evolution requires only that there be variation in populations. For the most part, that variation will either be in allele frequency, but sometimes is also mutational, sometimes due to neutral drift, and probably with considerably less frequency due to horizontal transfer. It ain't new, and neither is trying to make a well known phenomena sound exciting and "paradigm shifting" by announcing it to the world.

Man, but I hate science journalism.

Re:Well duh?

[CrimsonAvenger]

I can see that this might be plausible in the early stages of life on this planet where microbes would acquire genes from other microbes.

I saw an article recently about a species of snail that has acquired the genes for making chlorophyll from the algae it eats. It hasn't yet acquired the genes to make chloroplasts, so it has to eat algae to get enough chloroplasts from the algae to allow photosynthesis to work, but after that it is capable of living with no food other than light.

So, obviously this is still ongoing, and on larger scales than microbes.

Re:Gene Synthesis

[brit74]

It's not like one protein that catalyzes one reaction can simply mutate into a different protein that catalyzes a different reaction. It's more of an all or nothing thing. It doesn't seem like you would ever see transitional "evolutionary" forms of proteins for that reason.

There are instances of proteins evolving into something that does something different.

"Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species -- a shrew and a lizard -- giving each a venomous bite."
http://www.sciencedaily.com/releases/2009/10/091029125532.htm

Generally, what happens in these cases (where a protein evolved into a different protein with a different function) is that the original DNA sequence gets duplicated, and then one of the duplicates starts evolving (and the other copy continues to serve the same original function that it had earlier). One of the things that evolutionary biologists do is look at protein sequences and find similar sequences within the same organism. Very often, there's a tree-like structure showing multiple variations on a single protein within an organism. For example, humans have multiple copies/variations on the hemoglobin gene. They're either inactive or active at different phases in a person's life. Example:

"Fetal hemoglobin, or foetal haemoglobin, (also hemoglobin F or HbF) is the main oxygen transport protein in the fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream."
http://en.wikipedia.org/wiki/Hemoglobin_F
http://en.wikipedia.org/wiki/Hemoglobin#Types_in_humans

There's also the case of the fish antifreeze that evolved from non-protein-coding DNA:
"Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA."
http://www.sciencedaily.com/releases/2006/04/060404090831.htm

Re:Original paper on arXiv

[rgmoore]

This simply a lie, as is the claim that 64 combinations producing 20 codons is "redundancy". The reason there are only 20 is well-known to anyone with the least little bit of familiarity with the subject: it is the maximum number of unambiguous combinations, so that if you get six bases in a row there is exactly one way to read them, because no two codons together can result in a third codon being read between them.

Except that isn't true. Every one of the 64 possible 3 base sequences is a valid code for either an amino acid or a stop codon. Some viruses take advantage of this by overlapping protein coding regions, with different proteins being coded by reading in different frames. In eukaryotes, there are some genes that can code for proteins with very different sequence regions because an exon skipping splice variant results in a frame shift that codes for a completely different sequence.

A more significant complaint about the "This code is universal, shared by all organisms" quote is that it isn't universal. There are small differences in the genetic code between genomes. NCBI lists no fewer than 23 different versions, but given that a tiny fraction of all species have been studied there are undoubtedly many more minor variants. An especially interesting case- and the place that difference in genetic codes were first discovered- is that human nuclear and mitochondrial sequences use slightly different genetic codes. The mitochondria even have their own distinct ribosomes.

Re:You raise an interesting point here

[Opportunist]

Science is not the search for "truth". It's the search for an explanation. Unfortunately, it has become the new religion, people simply believe what some scientist says as gospel and, as you identified, are then frustrated and irritated if it is found to be incomplete or utterly false.

That is not how science is to be treated. Science does not have all the answers. Science is the search for those answers, not the answer itself. Science is not about believing, it is about doubting. About offering a theory and offering ways to test that theory. Especially the latter part is often overlooked by people. A good theory offers an angle to falsify it. I may state that at the center of a black hole is cake. Just to make all the Portal players happy. And while we're at it, before the big bang there was a flat world carried by a turtle. You cannot falsify either theory. You cannot test them. So they have to be true. Right? False! Both are non-theories. They have zero scientific value. At least until we somehow find ways to test them.

So presenting any theory that offers no vector of testing is, scientifically, worthless. Unfortunately, that's not easy to convey to people. They want explanations. And science cannot offer them. Science is not about certain answers. It is about questioning theories.

Re:Well duh?

[The End Of Days]

Creationism is ridiculed because creationism is ridiculous. Such posts get modded up because people with mod points agree, whether on topic or not. It's not really worth a sociology paper or anything.

If you really want to defend creationism on /., I salute your bravery. If you are just trying to figure out why people do what they do, I wish you tremendous amounts of luck.