Cell Size and Scale

If you ever wanted to better visualize the difference in size between a human cell, a bacterial cell, a virus, and an organelle, you should check out this nifty site.  Cool, eh?

Attempts to Refute Front-loading Part 2

We have seen that the first criticism of FLE has failed completely.  So let us now turn our attention to the second criticism. As it turns out, the second criticism is not really an argument against FLE, but is instead just a complaint.

Attempts to Refute Front-loading Part 1

In the previous posting, we saw that Brayton, MacNeill, and Neufeld all attempted to refute the hypothesis of front-loading evolution (FLE).  Yet in doing so, the three rely on only two basic arguments.  Let’s consider the first argument.

Brayton writes:

The other problem, of course, is that no one has ever found an organism that has all of the genes needed for later developments (feathers, wings, lungs, flagella, etc); that is, no organism actually has a fully complete genome front-loaded with all the goodies to be used later. If front loading was true, then the prokaryotes – the earliest existing life form on Earth – should have all of those genes. They don’t, of course.

And Neufeld makes the same argument:

For example, one can assume that God created the first life-form and put certain elements in its DNA that would eventually result in complex structures. It seems to me that this notion could be tested, because one should find apparent “junk” DNA in early creatures that looks like the DNA that creates complex structures in later life forms.

This argument fails.

Front-loading refuted?

If you google ‘front-loading evolution,’ there are three hits on the front and second page that attempt to refute this hypothesis.  Let’s have a look.

Intellectual honesty, misinformation, and cognitive dissonance

Previously I noted that my essay on intellectual honesty is still working its way through cyberspace. Today, I took the time to more carefully scan the replies/comments at Democratic Underground.  And while the overwhelming response was positive, there are a couple of comments worth responding to.

In one comment, a user with the handle RufusTFirefly spread some misinformation:

List originates (apparently) from a Web site called “Above Top Secret”

Here:
Above Top Secret

Further disseminated through a Web site called The Design Matrix (as in Intelligent Design) here:
The Design Matrix

RufusTFirefly has it backwards.  I wrote the essay and it was posted on my original Design Matrix blog and “Above Top Secret” was just one of the sites that further disseminated it.

Unfortunately, I cannot prove this simply and quickly because my original blog was hacked about a year ago and is now gone.  Nevertheless, there is more than enough evidence to establish I am correct.

Smart and Smarter

One of the expectations from the hypothesis of front-loading evolution is that cells would play a significant role in their own evolution, as this would constitute an intrinsic factor to evolution that would be more strongly connected to the original design event.  To this end, consider just how smart cells can be:

Scientists studying how bacteria under stress collectively weigh and initiate different survival strategies say they have gained new insights into how humans make strategic decisions that affect their health, wealth and the fate of others in society.

[…]

“We have developed for the first time a system level model of a large gene network to decipher the underlying principles of the bacteria game theory and how an internal network of genes and proteins is used to calculate risks in this complicated situation,” he said.

This has applications to human society because many people encounter similar dilemmas during their own lives. For example, should people ignore side effects and vaccinate against a new potentially lethal virus or should they not vaccinate and take the risk of being infected with the possible consequences? If the majority of the population is going to get vaccinated, then it is better for each individual not to get vaccinated. However, if most people will not be vaccinated then it is better to be vaccinated.

“What each bacterium is doing is the equivalent if each individual on earth was able receive the exact information about the rate of spread of this new virus, the exact information about the intensions, to be vaccinated or not, by each person on the planet, and in addition the exact information about the health risks of side effects or being infected,” said Ben Jacob. “A decision is then made in the context of this vast amount of information.”

“We have shown how the bacteria do this complex calculation according to well-defined principles,” added Onuchic. “We learned a simple rule: Anyone who needs to make a decision under pressure in life, especially if it is a possible death decision, will take its time. She or he will review the trends of change, will render all possible chances and risks, and only then react.”

And speaking of humans, consider this research:

A Special Fold?

A protein is a chain of amino acids that folds into a particular three dimensional conformation.  A fold is a particular conformation.  What science has discovered is that even though amino acid sequence variability is immense (for a protein of 100 amino acids there are 20^100 possible combinations, since there are 20 different amino acids), there are only  about 1000 or so shapes/folds that are employed by life.

You can think of a fold as a region where the amino acid chain is arranged into a scaffold.  Function is tied to the scaffold when it is decorated with an active site (which is usually some cleft or groove on the protein’s surface that binds a substrate and converts it to a product), and/or with other binding sites.

The immunoglobulin fold is a particular scaffold arrangement that is used to make antibodies (this scaffold is also found in many other proteins).

So I would like to pose a question that, as far as I have been able to determine, has never been asked.

Antibodies

Since I am going to be talking about antibodies, consider this video your homework assignment:

Speaking of viral….

Here

Intellectual honesty remains viral

My essay about intellectual honesty (originally posted on the original DM blog on October 20, 2008) continues to reverberate as can be seen here.