Monday, February 05, 2007

The Evolution of Life: Not What Your Momma Taught You

In biology I think we all pretty much take for granted the fact that all life on Earth is the evolutionary product of three distinct cell type lineages, the Bacteria, the Archaea, and the Eucarya, which were themselves the descendants of a common cellular ancestor (whose exact nature is now lost to us). This concept derives primarily from the so-called "universal phylogenetic tree" assembled based on a comparison of ribosomal RNA sequences of various types of cells. Indeed, the rRNA tree was one of the great accomplishments of the molecular era of biology, seeming to represent irrefutable evidence supporting Darwin's theories of common descent formulated a century or so earlier.

However, Carl Woese, who first came up with the universal rRNA phylogeny (also defined the Archaea as a new kingdom and originated the RNA world hypothesis), points out that the origin of life is not so clear cut. Although the rRNA tree gives a nice phylogeny that is agreeable with classical taxonomy, you run into problems when you start to try to compare trees based of sequences of different genes and proteins. For example, the Archaea and Eucarya might have the highest degree of homology when you compare gene A, but the Archaea might be more homologous to the Bacteria with respect to gene B. Apparently the frequency of these conflicts becomes more and more of an issue the further back you go through the tree, to the point where talking about three primitive and distinct cell types and trying to make inferences about their common ancestor doesn't even make any sense. Thus, he writes extensively about the need to develop and test new theories concerning the origins of cellular life. I've been checking out a few of his more recent reviews on the topic and they're pretty provacative and fun to read. Some interesting exerpts regarding the origins of cellular life:

The Annealing Model From The Universal Ancestor:

"A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result."

The Role of Horizontal Gene Transfer (from On The Evolution of Cells):

"A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given."

Other Carl Woese papers worth checking out:


rob said...

I don't understand how this concept applies to the phylogenetic tree of life, since prokaryotes predate eukaryotes by more than a billion years or so. I don't think they were the organisms that were exchanging anything.
Perhaps the precursors to prokaryotes did but quite obviously eukaryotes evolved much later from prexisting prokaryotes.
Also when you speak of the differences being different between geneA and geneB, just remember that there are well accepted explanations for this phenomenon. These genes are under selection and therefore are possibly differentially selected. Convergent evolution and sequence conservation can also explain these observations.
The articles you linked to sound very handwavy with unnecessarily large words and very little data.
"Cellular entities of this kind would not have stable genealogical records; this had to be a period of ephemeral organismal genealogies. The world of primitive cells feels like a vast sea, or field, of cosmopolitan genes flowing into and out of the evolving cellular (and other) entities. Because of the high levels of HGT, evolution at this stage would in essence be communal, not individual (63). The community of primitive evolving biological entities as a whole as well as the surrounding field of cosmopolitan genes participates in a collective reticulate evolution."
The world of primitive cells 'feels' like a vast sea....
I do agree however, after reading some more that a more complex model is required to adequately represent the phylogenetic relationships between the major primitive lineages of life that we have decided have a completely independant evolution, and it may involve some HGT.

Bayman said...

Yeah the prokaryote/eukaryote thing is an interesting debate as well...Woese is one who apparently believes the prokaryote designation, which groups the archaea and bacteria into a common lineage to be erroneous, although I haven't read much on the rationale...

Ben said...

Carl Woese is a cool dude. Very nice, very smart.

Anonymous Coward said...

Hey Ben, we were wondering if you were still reading the bayblab... Nice new look on your blog btw.

Ben said...

Haha. Why, thank you. I read every post. You folks seem to be a bit more focused than I am, however, which is generally a good thing.

Josh Greenberger said...

A deeper analysis of the underlying mechanism behind evolution and the fossil record, leaves little doubt that mutations of a random nature could not possibly have been the driving force behind the development of life on earth.

There has been opposition to the theory of evolution on the basis of whether a random process can produce organization. An analogy often given is, can a monkey on a typewriter, given enough time, produce the works of Shakespeare purely by random keystrokes? Let's assume for the purpose of this discussion that this is possible -- and that random mutations, given enough time, can also eventually produce the most complex life forms.

Let's begin by rolling a die (one "dice"). To get a "3," for example, you'd have to roll the die an average of six times (there are six numbers, so to get any one of them would take an average of six rolls). Of course, you could get lucky and roll a 3 the first time. But as you keep rolling the die, you'll find that the 3 will come up on average once every six rolls.

The same holds true for any random process. You'll get a "Royal Flush" (the five highest cards, in the same suit) in a 5-card poker game on average roughly once every 650,000 hands. In other words, for every 650,00 hands of mostly meaningless arrangements of cards (and perhaps a few other poker hands), you'll get only one Royal Flush.

Multi-million dollar lotteries are also based on this concept. If the odds against winning a big jackpot are millions to one, what will usually happen is that for every game where one person wins the big jackpot with the right combination of numbers, millions of people will not win the big jackpot because they picked millions of combinations of meaningless numbers. To my knowledge, there hasn't been a multi-million dollar lottery yet where millions of people won the top prize and only a few won little or nothing. It's always the other way around. And sometimes there isn't even one big winner.

How does this relate to evolution?

Let's take this well-understood concept about randomness and apply it the old story of a monkey on a typewriter. As mentioned earlier, for the purpose of this discussion, we'll assume that if you allow a monkey to randomly hit keys on a typewriter long enough he could eventually turn out the works of Shakespeare. Of course, it would take a very long time, and he'd produce mountains and mountains of pages of meaningless garbage in the process, but eventually (we'll assume) he could turn out the works of Shakespeare.

Now, let's say, after putting a monkey in front of a typewriter to type out Shakespeare, you decide you also want a copy of the Encyclopedia of Britannica. So you put another monkey in front of another typewriter. Then, you put a third monkey in front of third typewriter, because you also want a copy of "War And Peace." Now you shout, "Monkeys, type," and they all start banging away on their typewriters.

You leave the room and have yourself cryogenically frozen so you can come back in a few million years to see the results. (The monkeys don't have to be frozen. Let's say they're an advanced species; all they need to survive millions of years is fresh ink cartridges.)

You come back in a few million years and are shocked at what you see. What shocks you is not what you find, but what you don't find. First, you do find that the monkeys have produced the works of Shakespeare, the Encyclopedia of Britannica and "War and Peace." But all this you expected.

What shocks you is that you don't see the mountains of papers of meaningless arrangement of letters that each monkey should have produced for each literary work. You do find a few mistyped pages here and there, but they do not nearly account for the millions of pages of "mistakes" you should have found.

And even if the monkeys happened to get them all right the first time, which is a pretty big stretch of the imagination, they still should've type out millions of meaningless pages in those millions of years. (Who told them to stop typing?) Either way, each random work of art should have produced millions upon millions of meaningless typed pages.

This is precisely what the problem is with the Darwinian theory of evolution.

A random process, as depicted by Darwinian evolution and accepted by many scientists, even if one claims it can produce the most complex forms of life, should have produced at least millions of dysfunctional organisms for every functional one. And with more complex organisms (like a "Royal Flush" as opposed to a number 3 on a die), an even greater number of dysfunctional "mistakes" should have been produced (as there are so many more possibilities of "mistakes" in a 52-card deck than a 6-sided die).

The fossil record should have been bursting with billions upon billions of completely dysfunctional-looking organisms at various stages of development for the evolution of every life form. And for each higher life form -- human, monkey, chimpanzee, etc. -- there should have been millions of even more "mistakes."

Instead, what the fossil record shows is an overwhelming number of well-formed, functional-looking organisms, with an occasional aberration. Let alone we haven't found the plethora of "gradually improved" or intermediate species (sometimes referred to as "missing links") that we should have, we haven't even found the vast number of "mistakes" known beyond a shadow of a doubt to be produced by every random process.

We don't need billions of years to duplicate a random process in a lab to show that it will produce chaos every time, regardless of whether or not it might eventually produce some "meaningful complexity." To say that randomness can produce organization is one thing, but to say that it won't even produce the chaos that randomness invariably produces is inconsistent with established fact.

A process that will produce organization without the chaos normally associated with randomness is the greatest proof that the process is not random.

The notion that the fossil record supports the Darwinian theory of evolution is as ludicrous as saying that a decomposed carcass proves an animal is still alive. It proves the precise opposite. The relative scarcity of deformed-looking creatures in the fossil record proves beyond a doubt that if one species spawned another (which in itself is far from proven) it could not possibly have been by a random process.

To answer why we don't see many of the "mistakes" in the fossil record, some scientists point out that the genetic code has a repair mechanism which is able to recognize diseased and dysfunctional genetic code and eliminate it before it has a chance to perpetuate abnormal organisms.

Aside from this not being the issue, this isn't even entirely true. Although genetic code has the ability to repair or eliminate malfunctioning genes, many diseased genes fall through the cracks, despite this. There are a host of genetic diseases -- hemophilia, various cancers, congenital cataract, spontaneous abortions, cystic fibrosis, color-blindness, and muscular dystrophy, to name just a few -- that ravage organisms and get passed on to later generations, unhampered by the genetic repair mechanism. During earth's history of robust speciation (species spawning new ones) through, allegedly, random mutation, far more genes should have fallen through the cracks.

And, as an aside, how did the genetic repair mechanism evolve before there was a genetic repair mechanism? And where are all those millions of deformed and diseased organisms that should've been produced before the genetic repair mechanism was fully functional?

But all this is besides the point. A more serious problem is the presumption that natural selection weeded out the vast majority, or all, of the "misfits."

A genetic mutation that would have resulted in, let's say, the first cow to be born with two legs instead of four, would not necessarily be recognized as dysfunctional by the genetic repair mechanism. (I'll be using "cow" as an example throughout; but it applies to almost any organism.) From the genetic standpoint, as long as a gene is sound in its own right, there's really no difference between a cow with four legs, two legs, or six tails and an ingrown milk container. It's only after the cow is born that natural selection, on the macro level, eliminates it if it's not fit to survive.

It's these types of mutations, organisms unfit to survive on the macro level, yet genetically sound, that should have littered the planet by the billions.

Sure these deformed cows would have gotten wiped out quickly by natural selection, since they had no chance of surviving. But how many millions of dysfunctional cows alone, before you even get to the billions of other species in earth's history, should have littered the planet and fossil record before the first stable, functioning cow made its debut? If you extrapolate the random combinations from a simple deck of cards to the far greater complexity of a cow, we're probably talking about tens of millions of "mistakes" that should have cluttered planet earth for just the first functioning cow.

Where are all these relics of an evolutionary past?

Did nature miraculously get billions of species right the first time? Of the fossils well-preserved enough to study, most appear to be well-designed and functional-looking. With the low aberration ratio of fossils being no more significant, as far as speciation is concerned, than common birth deformities, there seems to have been nothing of a random nature in the development of life.

One absurd response I've gotten from a scientist as to why a plethora of deformed species never existed is: There is no such thing as speciation driven by deleterious mutation.

This is like asking, "How come everybody leaves the lecture hall through exit 5, but never through exit 4?" and getting a response, "Because people don't leave the lecture hall through exit 4." Wasn't this the question?

What scientists have apparently done is look into the fossil record and found that new species tend to make their first appearance as well-formed, healthy-looking organisms. So instead of asking themselves how can a random series of accidents seldom, if ever, produce "accidents," they've simply formulated a new rule in evolutionary biology: There is no such thing as speciation driven by deleterious mutation. This answer is about as scientific, logical and insightful as, "Because I said so."

It's one thing for the genetic code to spawn relatively flawless cows today, after years of stability. But before cows took root, a cow that might have struck us as deformed would have been no more or less "deleterious," from the genetic standpoint, than a cow that we see as normal. The genetic repair mechanism may recognize "healthy" or "diseased" genetic code, but it can't know how many legs or horns a completely new species should have, if we're talking about a trial-and-error crapshoot. If the genetic repair mechanism could predict what a functioning species should eventually look like, years before natural selection on the macro level had a chance to weed out the unfit, we'd be talking about some pretty weird, prophetic science.

In a paper published in the February 21, 2002, issue of Nature, Biologists Matthew Ronshaugen, Nadine McGinnis, and William McGinnis described how they were able to suppress some limb development in fruit flies simply by activating certain genes and suppress all limb development in some cases with additional mutations during embryonic development.

In another widely publicized experiment, mutations induced by radiation caused fruit flies to grow legs on their heads.

These experiments showed how easy it is to make drastic changes to an organism through genetic mutations. Ironically, although the former experiment was touted as supporting evolution, they both actually do the opposite. The apparent ease with which organisms can change so dramatically and take on bizarre properties, drives home the point that bizarre creatures, and bizarre versions of known species, should have been mass produced by nature, had earth's history consisted of billions of years of the development of life through random changes.

To claim that the random development of billions of life forms occurred, yet the massive aberrations didn't, is an absurd contradiction to everything known about randomness.

Evolutionists tend to point out that the fossil record represents only a small fraction of biological history, and this is why we don't find all the biological aberrations we should. But the issue here is not one of numbers but one of proportion.

For every fossil of a well-formed, viable-looking organism, we should have found an abundance of "strange" or deformed ones, regardless of the total number. What we're finding, however, is the proportional opposite.

Evolution may have made some sense in Darwin's days. But in the 21st century, evolution appears to be little more than the figment of a brilliant imagination. Although this imaginative concept has, in the years since Darwin, amassed a fanatical cult-like following, science, it is not. Science still needs to be proven; you can't just vote ideas into "fact." And especially not when they contradict facts.

One sign of the desperation of evolutionists to get their fallacious message across is their labelling of all disproofs of evolution as "Creationism," even when no mention of Creation or a deity is made. Ironically, it's evolutionists' dogmatic adherence to concepts that are more imagination than fact that smacks of a belief in mystical, supernatural powers. What evolutionists have done, in effect, is invented a new god-less religion and re-invented their own version of creation-by-supernatural-means. However, the mere elimination of God from the picture doesn't exactly make it science.

So if the development of life was not an accident, how did life come about?

Well, pointing out a problem is not necessarily contingent upon whether or not a solution is presented. In this case, presenting an alternative may actually be counterproductive. Evolutionists often get so bogged down with trying to discredit an proposed alternative, frequently with nothing more than invectives, that they tend to walk away believing evolution must still work.

The objective here, therefore, is to point out that Darwinian evolution does not fall apart because a solution being presented says it happened differently. The objective here is to show that the mechanics of evolution are incompatible with empirical evidence, verifiable science and common sense, regardless of whatever else may or may not take its place.

For a true study of science, we need to put the theory of evolution to rest, as we've done with so many other primitive concepts born of ignorance. Science today is far beyond such notions as metals that turn into gold, brooms that fly, earth is flat, and mystical powers that accidentally create life. What all these foolish beliefs have in common is that they were popular in their own time, were never duplicated in a lab, and were never proven by any other means.

We'd be doing society a great service if we filled our science textbooks with verifiable facts that demonstrate how science works, instead of scintillating fabrications that demonstrate how imaginative and irrational some scientists can get.