Latest Challenges to the Teaching of Evolution

I know fm. You just declare yourselves to be wonderful and, hey presto, you are. It's brilliant I must admit

. . . And for Licetus Fortunio . . . all the world knows he was born a foetus. [He] was no larger than the palm of the hand, five and one half inches, but the father, having examined it in his medical capacity, and having found that it was something more than a mere embryo, brought it living to Rapallo, where it was seen by Jerome Bardi and other doctors of the place. They found it was not deficient in anything essential to life, and the father, in order to show his skill, undertook to finish the work of nature and to perfect the formation of the infant by the same artifice as is used in Egypt for the hatching of chickens. He instructed a wet-nurse in all she had to do, and having put his son in an oven, suitably arranged, he succeeded in rearing him, and in making him take on the necessary increase of growth, by the uniformity of the external heat, measured accurately in the degrees of a thermometer, or other equivalent instrument.

One would still have to be very satisfied with the industry of a father so skilled in the art of generation, had he been able to prolong his son's life for no more than a few months or a few years.
But when one considers that the child lived nearly eighty years, and that he composed twenty-four different works, each the fruit of long reading, one must acknowledge that all that is incredible is not always false, and that appearance is not always on the side of truth.
He was only nineteen when he composed Gonopsychanthropologia de Origine Animae humanae.

Self-Assembly of the Bacterial Flagellum: No Intelligence Required
(Kathryn Applegate, The BioLogos Forum, August 19, 2010)

In my last post, I explained why the bacterial flagellum remains so powerful an icon for the Intelligent Design (ID) movement: it looks and functions just like the outboard motor, a machine designed by intelligent human engineers. So conspicuous is the resemblance that it seems perfectly logical to infer a Designer for the flagellum.

Yet as we saw, appearances can be deceiving. ID advocates William Dembski and Jonathan Witt agree that “a careful investigator will be on guard against deceiving appearances. The sun looks like it rises in the east and sets in the west, but really the Earth spins on its axis as it revolves around the sun. A healthy skepticism about appearances is vital…To distinguish appearance from reality, the successful investigator must remain open to various possibilities and follow the evidence.”

Despite the strong appearance of special design, most scientists, myself included, believe the evidence points to a gradual development for the bacterial flagellum. We’ll delve into some of that evidence in future posts. First, however, I want to explain how flagella are assembled in bacteria. This amazing process gives me such delight in our Father’s world; I hope it does for you as well.

The bacterial flagellum may look like an outboard motor, but there is at least one profound difference: the flagellum assembles spontaneously, without the help of any conscious agent. The self-assembly of such a complex machine almost defies the imagination. As I showed with an earlier blog on the self-assembly of viruses (much simpler contraptions by comparison), all such phenomena seem astonishing and counterintuitive.

Because the tail of the flagellum extends well beyond the bacterial cell wall, many of its 40 or so components have to be extruded through an export apparatus that assembles first and makes up the base of the final structure. In general, assembly occurs as a linear process, with components in the base coming together first, followed by the formation of the hook, followed by formation of the filament.

First, the MS-ring assembles in the inner cell membrane, most likely in conjunction with some of the export proteins. The MS-ring serves as housing for the export apparatus and as a mounting plate for the rotor, which will assemble later.

Next, the stator assembles around the MS-ring, followed by the rotor. The stator remains fixed in the cell’s frame of reference, while the rotor spins; together, these two parts make up the proton-powered motor.

Now that the base of the flagellum is built, most of the remaining parts are assembled from proteins exported through its center. First comes the rod, made of four different kinds of proteins, guided by a fifth, the “rod cap,” which is believed to help break down the tough bacterial cell wall.

This “rod cap” is then displaced by a “hook cap,” which guides the formation of the hook structure. The hook acts as a universal joint to connect the rod and the filament. When the hook reaches its characteristic length, several “junction zones” form, followed by the export of the “filament cap” protein. This cap structure, different than the rod or hook caps, guides the bundling of more than 20,000 copies of a protein called flagellin into a helical tail.

The helical filament is long and fragile, but breakage is not too serious a concern for the bacterium. Like a lizard, the flagellum can grow a new tail if it breaks, because flagellin proteins continue to move down the central channel from the cell body toward the tip. Other parts of the flagellum are dynamic as well: individual proteins in the rotor and stator, for example, can exchange with freely-diffusing proteins in the membrane. Such activity may be important for the bacterium’s direction-sensing capability.

Scientists are pretty clever at teasing out the workings of microscopic machines like the flagellum. The general order of assembly was meticulously worked out by removing individual protein components one at a time and observing what occurred. If you remove the flagellin protein, for instance, you get the base and the hook, but not the tail. This tells us that the tail forms late in the assembly process. If you remove one of the proteins that make up the MS-ring, on the other hand, the motor elements do not assemble and neither does the rest of the flagellum. That’s how we know the MS-ring isn’t just tacked on at the end.

Other scientists have looked at how the timing of the assembly process is controlled at the genetic level. The genes that contain the instructions for making all the protein components of the flagellum are organized in a number of clusters called operons. Each operon is read when its “master sequence” is activated like a light switch. When the switch is flipped, the genes in that particular operon are interpreted by the cell so that the corresponding proteins are made. It turns out that the genes needed to produce proteins in the base of the flagellum are activated first. Once the base is complete, a clever feedback mechanism flips the next switch, activating the next set of genes, which allows later stages of assembly to occur, and so on. (It’s actually more complicated than that, but you get the idea.) So the parts of the flagellum are made “just in time,” shortly before each piece is needed.

Nothing we know from every day life quite prepares us for the beauty and power of self-assembly processes in nature. We’ve all put together toys, furniture, or appliances; even the simplest designs require conscious coordination of materials, tools, and assembly instructions (and even then there’s no guarantee that we get it right!). It is tempting to think the spontaneous formation of so complex a machine is “guided,” whether by a Mind or some “life force,” but we know that the bacterial flagellum, like countless other machines in the cell, assembles and functions automatically according to known natural laws. No intelligence required.

Several ID advocates, most notably Michael Behe, have written engagingly about the details of flagellar assembly. For that I am grateful—it is wonderful when the lay public gets excited about science! But I worry that in their haste to take down the theory of evolution, they create a lot of confusion about how God’s world actually operates.

When reading their work, I’m left with the sense that the formation of complex structures like the bacterial flagellum is miraculous, rather than the completely normal behavior of biological molecules. For example, Behe writes, “Protein parts in cellular machines not only have to match their partners, they have to go much further and assemble themselves—a very tricky business indeed” (Edge of Evolution, 125-126). This isn’t tricky at all. If the gene that encodes the MS-ring component protein is artificially introduced into bacteria that don’t normally have any flagellum genes, MS-rings spontaneously pop up all over the cell membrane. It’s the very nature of proteins to interact in specific ways to form more complex structures, but Behe makes it sound like each interaction is the product of special design.

Ive seen it happen so often with your brother hillbillies

Im betting that its because you need to try to constantly speak in a derogatory fashion of people who are better educated than you or who have a skill that you wish youd had.

You have assumed :
1) you have skill Not an assumpion , its a fact
2) that I dontsee above
3) that I wish I was you (hahahahahaha) first youd need a skill
4) I was derogatory and not factual your history supports my claim
5) You have never done anything to deserve my derogatory responseI know you dont appreciate having your mistakes shown in public, does that count ?
6) You are better educated than me..... without any fear of doubt

Well, you got it half right.

Which half ? What do whales have to do with my example ? They went the other way, losing their legs. Did you understand or not ?

If you want to understand evolution it involves gradual change to an environment producing gradual change in species when suddenly there is an opening for expansion. An example is the development of legs before moving onto land. Suddenly a whole new opportunity was available to a species that had legs.

You were talking as if the organisms went and "ventured" into the new environment. It was much simpler, the environments were rapidly changing around them so they evolved or went extinct.

Darwin wrong—again??
(Jerry Coyne, Why Evolution Is True Blog, August 26, 2010)

You may have seen a small flurry of reports this week about a science paper showing that “Darwin was wrong.” The paper wasn’t a creationist or ID screed, however—it was a paper in a good science journal (Biology Letters) by a crack team of paleontologists from the UK and Canada (Sarda Sahney, Michael Benton, and Paul Ferry). What did the paper say? Did it really show that Darwin was wrong? I’m here to answer your questions.

What did the paper say? It reported a correlation in the fossil record between the number of tetrapods (four-legged vertebrates) existing at different times and the number of ecological ” modes of life” those species adopted, all over the 400-million-year period since vertebrates colonized the land. To be exact, it divided up that time period into 66 sub-periods, and in each sub-period the authors totted up the number of tetrapod families that were represented by fossils and the number of modes of life they adopted.

The authors defined a “mode of life” as the ecology of a species that fit into one of three body size categories (length less than 15 cm, between 15 and 150 cm, and greater than 150 cm), one of 16 diet categories (browser, nectar, molluscs, carrion, and so on), and one of 6 habitat categories (marine, arboreal, subterranean, and so on). This gave 288 potential modes of life (3 x 16 x 6), only 75 of which were actually seen.

The authors interpret the tight fit between biodiversity (number of families) and ecological diversity (number of modes of life seen among those families) to mean that what drove tetrapod diversity over this period was open niche space: ecological opportunities that had not yet been realized. They oppose this to another explanation that, they say, their data did not support: diversification was driven not by the availability of ecological space, but by competition. The competition theory would, say the authors, predict that as organisms began to lose elbow room, they would simply subdivide their already-occupied “modes of life” into finer ones. If competition drove diversification, then, you wouldn’t see such a tight correlation between modes of life and diversity.

Is this interpretation correct? I’m not so sure. The problem is that it might not be possible to separate the “force” of competition from the selective pressure to occupy new niches. After all, animals may be driven to adopt new modes of life by competition itself. The occupation of the land by ancestral fish may, for example, have been the result of selection to reduce competition for prey by finding a nice new place with lots of prey (insects) and fewer competititors. I don’t think that showing a correlation between “modes of life” and “number of families” tells us that competition did not play a big role in driving that diversity. In other words, I am not convinced that, at least from the fossil data, you can separate competition from ecological opportunity.

Also, it’s possible that some of the correlation is an artifact. It may be—and I’m not sure of this because I’m not a paleobiologist—that different taxonomic families are partially recognized by large differences in characters like body size and adaptations to diet or habitat. In that case you only get a new family when there’s a sufficiently large difference in what we’d recognize as a “mode of life.” This would be true regardless of the evolutionary force driving the difference. And to the extent that this is the case, it devalues the correlation as a way to recognize process.

This doesn’t mean the paper is bad. Far from it—it’s a very good (and laborious!) correlation between ecology and diversity, and the correlations between them do demand explanation. I’m just not sure if the authors’ answer is the right one.

Where did the “Darwin was wrong” stuff come from? It comes from the notion that Darwin saw competition as a major cause of ecological diversity. There is some justification for this: in The Origin, for example, the only figure (the famous “tree of life”) shows an increase in diversity over time, with Darwin attributing this to competition between species for niche space. His “principle of divergence” maintained that organisms inhabiting a small area would always be competing with each other, and would benefit by seizing on slightly different niches to reduce that competition. A grass, for example, might inhabit soils of different moisture content to avoid competing for space with other grasses.

We shouldn’t think, though, that Darwin saw competition as the overweening force in promoting biological diversity. In The Origin he adduces other factors, including simple adaptation to physical factors (“a plant on the edge of a desert is said to struggle for life against the drought”), and to biotic features like predators and parasites. I think that Darwin may have seen biotic factors as a whole (which include but are not limited to competition), as important drivers of diversity, and emphasized them so that his readers would see that natural selection didn’t solely promote responses to the physical, non-biotic environment.

So did the paper show that Darwin was wrong? Hardly. As I said above, I don’t think the authors ruled out competition as an important force in ecological diversity. Indeed, you could almost construe the data as supporting Darwin, who emphasized throughout The Origin that the more different species were, the better their chances of leaving descendants. (See pp. 111-125 of the first edition of The Origin for this view.) He emphasizes, for instance, that plants have a better chance of invading a new area if they were already quite different from the species that were already there.

But of course Darwin was wrong about many things. Nobody pretends that the man was a god, or omniscient. He was dead wrong, for instance, about genetics. We know a lot more about biology now than we did in Darwin’s time, and we can see that his ideas were often incomplete or incorrect. So it’s bizarre to see every modern discovery through a lens of either supporting or refuting his ideas. If we did that, every paper in genetics could be sold to science journalists as showing that Darwin was wrong about inheritance! We’ve moved on. It’s amazing how right Darwin was—that’s one of the reasons he’s a hero to many of us—but, like all scientists, his ideas get supplanted and revised.

Why did the press sell the paper this way? Hype, pure and simple. A paper on taxonomic diversity over time gets a lot more interest if it can be said to disprove Darwin. I suppose there’s some residual anti-evolution or anti-Darwin sentiment in all this.

Who’s responsible for this hype? I’d like to think it was just the press, for they always love a controversy. But I’m curious how all these different journalists managed to hit on the same Darwin-was-wrong hook. Are a lot of science journalists really conversant enough with Darwin to immediately and independently see a Biology Letters paper as refuting his ideas? Well, maybe one of them did it and was copied by the others. But I wonder whether the authors, or the authors’ universities, or even the journal, issued a press release that sold the paper as a “Darwin refuter.”

Indeed, you could almost construe the data as supporting Darwin, who emphasized throughout The Origin that the more different species were, the better their chances of leaving descendants.

HERE IS WISDOM=66//AND HIS NUMBER IS=66///SPIRIT OF GOD=66///DIE AND TELL ABOUT IT=66 LIFE AFTER DEATH=66 RESURRECTION=66//THE HONEST TRUTH=66 THE WHOLE TRUTH=66 THE ALMIGHTY SATAN=66 RULER OF EARTH=66 THE TIME IS AT HAND=66=6+6=12 and half=6 add 12 to 6=18:6,6,6.//// saint=18 avatar=18 love=18 come=18 I AM THE LORD OF HOSTS BEHOLD HOSTS=18:6,6,6 HOLY,HOLY HOLY=6,6,6 HOLY=24=2+4=6 TRUTH=24,FOR HOLY IS THE TRUTH