Tag: evolution

Fred Reed, who is “a thoroughgoing agnostic”, poses a few questions based on his inferences from observation for the advocates of the Theorum of Evolution by (mostly) Natural Selection In Addition To A Panoply of Less Famous Evolutionary Mechanisms:

Over the years I have occasionally expressed doubts over the tenets of evolutionism which, perhaps wrongly, has seemed to me a sort of political correctness of science, or maybe a metaphysics somewhat related to science. As a consequence I have been severely reprimanded. The editor of a site devoted to genetic expression furiously began deleting any mention of me from his readers. Others, to include Mr. John Derbyshire of Taki’s Magazine, have expressed disdain, though disdaining to explain just why.

In all of this, my inability to get straight answers that do not shift has frustrated me. I decided to address my questions to an expert in the field, preferably one who loathed me and thus might produce his best arguments so as to stick it to me. To this end I have settled on Mr. Derbyshire….

1. what selective pressures lead to a desire not to reproduce, and how does this fit into a Darwinian framework?
2. Why should I not indulge my hobby of torturing to death the severely genetically retarded?
3. How many years would have to pass without replication of the [Abiogenesis]
   event, if indeed it be not replicated, before one might begin to suspect
   that it didn’t happen? 
4. What are the viable steps needed to evolve from [two-cycle insect] to [four-cycle insect]? Or from anything to four-cycle? 
5. Does not genetic determinism (with which I have no disagreement) lead to a paradox: that the thoughts we think we are thinking we only think to be thoughts when they are really utterly predetermined by the inexorable working of physics and chemistry? 
6. Why do seemingly trivial traits proliferate while clearly important ones do not?
7. If one believes in or suspects the existence of God or gods, how
   does one exclude the possibility that He, She, or It meddles in the
   universe—directing evolution, for example?  

Of course, anyone here who still subscribes to believe in abiogenesis and evolution by natural selection is more than welcome to take a crack at one or more of these themselves. However, before answering any of them, I would highly recommend reading the complete article, as Fred goes into more details regarding why he is asking each of the questions there.

Dr. James M. Tour of Rice University confesses he simply cannot grasp what everyone at Scienceblogs and the Panda’s Thumb and Richarddawkins.net just knows to be true. Because science.

I will tell you as a scientist and a synthetic chemist: if anybody should be able to understand evolution, it is me, because I make molecules for a living, and I don’t just buy a kit, and mix this and mix this, and get that. I mean, ab initio, I make molecules. I understand how hard it is to make molecules. I understand that if I take Nature’s tool kit, it could be much easier, because all the tools are already there, and I just mix it in the proportions, and I do it under these conditions, but ab initio is very, very hard.

I don’t understand evolution, and I will confess that to you. Is that OK, for me to say, “I don’t understand this”? Is that all right? I know that there’s a lot of people out there that don’t understand anything about organic synthesis, but they understand evolution. I understand a lot about making molecules; I don’t understand evolution. And you would just say that, wow, I must be really unusual.

Let me tell you what goes on in the back rooms of science – with National Academy members, with Nobel Prize winners. I have sat with them, and when I get them alone, not in public – because it’s a scary thing, if you say what I just said – I say, “Do you understand all of this, where all of this came from, and how this happens?” Every time that I have sat with people who are synthetic chemists, who understand this, they go “Uh-uh. Nope.” These people are just so far off, on how to believe this stuff came together. I’ve sat with National Academy members, with Nobel Prize winners. Sometimes I will say, “Do you understand this?”And if they’re afraid to say “Yes,” they say nothing. They just stare at me, because they can’t sincerely do it.

I was once brought in by the Dean of the Department, many years ago, and he was a chemist. He was kind of concerned about some things. I said, “Let me ask you something. You’re a chemist. Do you understand this? How do you get DNA without a cell membrane? And how do you get a cell membrane without a DNA? And how does all this come together from this piece of jelly?” We have no idea, we have no idea. I said, “Isn’t it interesting that you, the Dean of science, and I, the chemistry professor, can talk about this quietly in your office, but we can’t go out there and talk about this?”

If you understand evolution, I am fine with that. I’m not going to try to change you – not at all. In fact, I wish I had the understanding that you have.

But about seven or eight years ago I posted on my Web site that I don’t understand. And I said, “I will buy lunch for anyone that will sit with me and explain to me evolution, and I won’t argue with you until I don’t understand something – I will ask you to clarify. But you can’t wave by and say, “This enzyme does that.” You’ve got to get down in the details of where molecules are built, for me. Nobody has come forward.

The Atheist Society contacted me. They said that they will buy the lunch, and they challenged the Atheist Society, “Go down to Houston and have lunch with this guy, and talk to him.” Nobody has come! Now remember, because I’m just going to ask, when I stop understanding what you’re talking about, I will ask. So I sincerely want to know. I would like to believe it. But I just can’t.

Now, I understand microevolution, I really do. We do this all the time in the lab. I understand this. But when you have speciation changes, when you have organs changing, when you have to have concerted lines of evolution, all happening in the same place and time – not just one line – concerted lines, all at the same place, all in the same environment … this is very hard to fathom.

I was in Israel not too long ago, talking with a bio-engineer, and [he was] describing to me the ear, and he was studying the different changes in the modulus of the ear, and I said, “How does this come about?” And he says, “Oh, Jim, you know, we all believe in evolution, but we have no idea how it happened.”

Smells like quality science. And before the usual science fetishists leap in to assert the obvious and declare: “yeah, well, that doesn’t prove God exists,” I will readily admit that it does not. But, (and here is the point), it does prove that there are very rational reasons to doubt the unevidenced assertion that “evolution is a fact”.

As I have repeatedly pointed out, I am an evolution skeptic, not an evolution denier. I do not judge the truth of the belief by the behavior of the believer, although if I did, the behavior of the evolutionary true believers would be sufficient to convince me that the existence of unicorns, fairies, and leprechauns combined is considerably more likely than fish magically turning into monkeys over time due to beneficial mutations taking advantage of the multitude of changes in the water.

It is remarkable how evolution enthusiasts can’t seem to reach the logical conclusion concerning their repeated inability to successfully debate creationists. Then again, if they had as solid a grasp on logic and statistics as they do on the various epicycles of their ever-evolving “theory”, they would not be evangelical evolutionists in the first place:

In a much-hyped showdown, “the Science Guy” tried to defend evolution against creationist Ken Ham, and proved how slick science-deniers can be. How did the guy who’s right go so wrong?

On many mornings, I wake up and think, “You know what this country needs? More culture war.” As I scramble up a couple eggs, I find myself wishing—fervently wishing—that we could spend more time reducing substantive issues to mere spectacle. Later, as I scrub the pan, I’ll fantasize about how those very spectacles might even funnel money toward some of the country’s most politicized religious groups.

Fortunately, Bill “the Science Guy” Nye has heard my wish—which, really, is the wish of a nation. Why else would he have traveled to Kentucky this week in order to debate Ken Ham, the young-earth creationist founder of Answers in Genesis, about the origins of the world?

Actually, there are two other reasons that Nye might have done so, and I’ve given both possibilities a great deal of thought in the past few days. The first is that Nye, for all his bow-tied charm, is at heart a publicity-hungry cynic, eager to reestablish the national reputation he once had as the host of a PBS show. When his stint on Dancing With the Stars ended quickly, Nye turned to the only other channel that could launch him back to national attention: a sensationalized debate, replete with the media buzz that he craves.

Possibility number two is that Nye is clueless—that, for all his skill as a science communicator, Nye has less political acumen than your average wombat.

After watching the debate, I’m leaning toward that second possibility. Last night, it was easy to pick out the smarter man on the stage. Oddly, it was the same man who was arguing that the earth is 6,000 years old. It was like watching the Broncos play the Seahawks. Nye never had a chance.

I didn’t watch the “debate”. I had no interest in it, surmising correctly, (as it turns out), that neither side would actually be debating, but were instead engaged in mutual preaching to their own choirs. And it is amusing to observe the wrestling with the temptation intellectual dishonesty poses to the evolutionists as a result of their frustration with their own inability to successful defend their faith

For example, the writer claims it is bullshit to distinguish between scientific evidence and historical extrapolation. He asserts: “We can use evidence from the present to extrapolate about the past.” Well, yes, but that doesn’t disprove Ham’s point, which isn’t so much a point as a basic fact. An extrapolation is not, by definition, an observation. Nor can a historical extrapolation be tested.

For some reason, science fetishists who understand very well that it is impossible to use science to prove that Abraham Lincoln succeeded George Washington as president do not understand that it is equally impossible to use science to prove that species X transformed into species Y. Extrapolation only takes us to the hypothesis part of the scientific equation, it does not get us past the necessary testing and observation aspects. Barring a time machine, it is history, not science.

And in the end, the author throws in the towel, admits defeat, and advocates a full-blown retreat:

You don’t need to be Sun Tzu to realize that, when it comes to guys like Ken Ham, you can’t really win. If you refuse to debate them, they claim to be censored. If you agree to debate them, you give them a public platform on which to argue that, yep, they’re being censored. Better not to engage at all, at least directly.

Needless to say, the side that dares not directly engage is the side that knows it cannot successfully make its case. And the more the evangelical Darwinians appeal to an increasingly threadbare scientific authority, the weaker their case is observed to be by all impartial parties. When they’re saying: “you don’t understand the biology” and their critics are saying: “you don’t understand the math”, well, as it turns out, we have an excellent means of determining whose claims are founded in fact and whose are not.

And what we can readily test and observe with these two competing hypotheses is that the scientific evidence here does not favor those appealing to scientific authority.

I find it remarkable that despite this apparent order of magnitude, (or more), change in the complexity of the DNA code, (now codes), even the genetic scientists who made the discovery are failing to grasp its obvious implications with regards to conventional Neo-Darwinian selectionism:

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code is similar for all organisms and is stored in one of the two DNA strands as non-overlapping, linear sequence of nitrogenous bases Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). These four letters are the ‘alphabet’ of the genetic code and are used to write code words. The code consists of three-letter words (also called triplets or codons). There are a total of 64 codons.

Now, researchers have found that the codons, which they refer to as duons, can be used for gene control. The team says that about 15 percent of codons could act as duons and that these bilingual genetic codes have shaped protein evolution.

At this point, one is beginning to wonder if the scientists are so focused on the evolutionary trees that even a copyright notice would somehow escape their attention. Copyright (c) 6000 BC God. All rights reserved. “Well, obviously that is a codal pattern that evolved early in a common ancestor and merely happens to look like alphabetical characters, from which the various divergent mutations didn’t happen to provide any selection advantages.”

Here is the point that so many die-hard evolutionists can’t seem to grasp. Let me try to walk them through the logic of my skepticism with a simple analogy.

Charlie has a car. Charlie is speaking to you in Minneapolis. Charlie says he left Chicago seven hours ago and drove to Minneapolis on a single tank of gas. However, in the car, you discover two receipts, both dated today, from gas stations in Colorado Springs and Sioux Falls.

Now, if you can understand how this indicates that Charlie’s story is false, you should be able to understand how adding an additional order of magnitude of complexity to the DNA programming process completely rules out the time-scale of the conventional Neo-Darwinian selectionist model. There were already real problems with the model, hence the development of hypothesized excuses such as Punctuated Equilibrium.

But by adding the time needed for another level of mutation on top of what was already required by the previous single-code model, I don’t see how it is possible to seriously insist that the conventional natural selection model can hold up in light of this discovery. Now, perhaps I’m missing something, but it seems to me that either the DNA mutation process has to take place considerably faster than has been observed over the past 50 years or a new model will be required.

My guess is that the initial explanatory defense will be that the mutations are more frequent, but more significant using the two-code process, but this is a defense unlikely to do more than buy a little time, as it will soon be possible to observe whether such mutations are actually taking place or not. Remember, the main reason that TENS has been able to survive so long is that its long timescales required resisted observation. If the timescales are shorter and the mutations selected more frequent, then we can observe and falsify them.

And, of course, even if the new, faster model turns out to be correct, this opens up a whole new can of worms that Jonathan Haidt correctly identifies as the likely consequences of a faster evolutionary model:

A wall has long protected respectable evolutionary inquiry from accusations of aiding and abetting racism. That wall is the belief that genetic change happens at such a glacial pace that there simply was not time, in the 50,000 years since humans spread out from Africa, for selection pressures to have altered the genome in anything but the most trivial way (e.g., changes in skin color and nose shape were adaptive responses to cold climates). Evolutionary psychology has therefore focused on the Pleistocene era – the period from about 1.8 million years ago to the dawn of agriculture — during which our common humanity was forged for the hunter-gatherer lifestyle. But the writing is on the wall.

It should be interesting to see how those who are true believers in both a) the religion of TENS and b) the myth of human equality react to this scientific claim from Penn State that Africans are less evolved than Europeans:

Light skin in Europeans stems from a gene mutation from a single person who lived 10,000 years ago. This is according to a new U.S. study that claims the colour is due to an ancient ancestor who lived somewhere between the Middle East and the Indian subcontinent. Scientists made the discovery after identifying a key gene that contributes to lighter skin colour in Europeans.

In earlier research, Keith Cheng from Penn State College of Medicine reported that one amino acid difference in the gene SLC24A5 is a key contributor to the skin colour difference between Europeans and West Africans. ‘The mutation in SLC24A5 changes just one building block in the protein, and contributes about a third of the visually striking differences in skin tone between peoples of African and European ancestry,’ he said.

We already know that the three major continental groups are not even equally human on the genetic level, with Africans being the only pure homo sapiens sapiens. This new claim indicates that Africans are lower in the evolutionary order, not that the skin color gene can be described as a speciation event. Regardless, one wonders why those who stubbornly, and ignorantly, continue to insist on human equality despite these undeniable genetic differences which are much more than skin deep are not yet tarred by the label “science denier”.

What I find amusing is that the scientists have already leaped in with some strained explanations to cram natural selection into the process when it is very clear from modern human behavior that the rapidity of the growth of the mutation would much more likely have stemmed from sexual selection. There need not be any environmental advantage to lighter skin for it to be preferred. Of course, that would also be a hate fact, as it would be scientific evidence that whites are more attractive than blacks. That being said, a fact is a fact.

However, that’s not the intriguing stuff. Here’s a much more interesting thought. The 10,000 year time frame is not all that far off from Bishop Usher’s famous 6,000 year estimation for the Age of the Earth. But most forget that the bishop’s estimate was based on Adam, not the Earth. So, what if it can eventually be determined that the single genetic mutation was actually an artificial one? That would certainly set the cat among the equality pigeons.

As usual, I appear to be well in advance of the scientists. Isn’t it simply astonishing that a non-scientist can so readily and reliably predict the inaccuracy and unreliability of the current scientific consensus? How is that even theoretically possible? How can ignorance trump credentials and actual science education? And yet….

In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years.

The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.

The mismatch between the anatomical and genetic evidence surprised the scientists, who are now rethinking human evolution over the past few hundred thousand years. It is possible, for example, that there are many extinct human populations that scientists have yet to discover. They might have interbred, swapping DNA. Scientists hope that further studies of extremely ancient human DNA will clarify the mystery.

There isn’t a mystery here. The TENS true believers keep thinking that genetics will color in the lines of their rudimentary evolution-based models, but instead, the science keeps breaking their lines. All of the conceptual models are wrong. Pretty much all of the carefully calculated timelines are wrong. Evolution by natural selection is a red herring of a theory that was developed at a time when the scientific tools were crude and largely unscientific. So, it should be absolutely no surprise that the improved data being provided by advancements in genetic science is repeatedly overturning the conclusions that were previously reached.

Mendel didn’t expose the physical gene, of course (that would come a
century later), but the conceptual gene. And this conceptual gene,
revealed in the tables and calculations of this math-friendly monk,
seemed an agent of mathematical neatness. Mendel’s thousands of
crossings showed that the traits he studied — smooth skin versus
wrinkled, for instance, or purple flower versus white — appeared or
disappeared in consistent ratios dictated by clear mathematical
formulas. Inheritance appeared to work like algebra. Anything so
math-friendly had to be driven by discrete integers.
It was beautiful work. Yet when Mendel first published his findings in 1866, just seven years after Charles Darwin’s On the Origin of Species,
no one noticed. Starting in 1900, however, biologists rediscovering his
work began to see that these units of heredity he’d discovered — dubbed
genes in 1909 — filled a crucial gap in Darwin’s theory of evolution. This recognition was the Holy Shit! moment that launched genetics’ Holy Shit! century. It seemed to explain everything. And it saved Darwin.

Darwin had legitimised evolution by proposing for it a viable
mechanism — natural selection, in which organisms with the most
favourable traits survive and multiply at higher rates than do others.
But he could not explain what created or altered traits. Mendel could. Genes created traits, and both would spread through a
population if a gene created a trait that survived selection….

These days, Dawkins makes the news so often for buffoonery that some might wonder how he ever became so celebrated. The Selfish Gene
is how. To read this book is to be amazed, entertained, transported.
For instance, when Dawkins describes how life might have begun — how a
randomly generated strand of chemicals pulled from the ether could
happen to become a ‘replicator’, a little machine that starts to build
other strands like itself, and then generates organisms to carry it — he
creates one of the most thrilling stretches of explanatory writing ever
penned. It’s breathtaking.

Dawkins assembles genetics’ dry materials and abstract maths into a
rich but orderly landscape through which he guides you with grace,
charm, urbanity, and humour. He replicates in prose the process he
describes. He gives agency to chemical chains, logic to confounding
behaviour. He takes an impossibly complex idea and makes it almost
impossible to misunderstand. He reveals the gene as not just the centre
of the cell but the centre of all life, agency, and behaviour. By the
time you’ve finished his book, or well before that, Dawkins has made of
the tiny gene — this replicator, this strip of chemicals little more
than an abstraction — a huge, relentlessly turning gearwheel of steel,
its teeth driving smaller cogs to make all of life happen. It’s a
gorgeous argument. Along with its beauty and other advantageous traits,
it is amenable to maths and, at its core, wonderfully simple.

Unfortunately, say Wray, West-Eberhard and others, it’s wrong.

The best part of all this is that Dawkins clearly knows it’s wrong too. Not that he’s going to admit it, though, not yet.

I phoned Richard Dawkins to see what he thought of all this. Did
genes follow rather than lead? I asked him specifically about whether
processes such as gene accommodation might lead instead. Then he did
something so slick and wonderful I didn’t quite realise what he’d done
till after we hung up: he dismissed genetic accommodation… by
accommodating it. Specifically, he said that genetic accommodation
doesn’t really change anything, because since the gene ends up locking
in the change and carrying it forward, it all comes back to the gene
anyway.

‘This doesn’t modify the gene-centric model at all,’ he said. ‘The
gene-centric model is all about the gene being the unit in the hierarchy
of life that is selected. That remains the gene.’

‘He’s backfilling,’ said West-Eberhard. ‘He and others have long been
arguing for the primacy of an individual gene that creates a trait that
either survives or doesn’t.’

They backtest and they backfill. That’s due to the crumbling state of TENS. They’re still clinging to natural selection, of course. But the TENS model is in crisis and it will collapse soon enough. It is even beginning to look as if we may get to see it happen in our lifetimes. Gene expression is more compatible with Intelligent Design than with TENS. We are not evolved, we are created. DNA is our C++ equivalent, and the womb is our compiler. Compile it differently, get different results. This is not New Age mumbo jumbo, but a scientific hypothesis that will be testable once we understand it well enough to become proficient in programming it ourselves.