Scientists have long known what drives the flagellum to spin, but what causes the flagellum to stop spinning — temporarily or permanently — was unknown.
“We think it’s pretty cool that evolving bacteria and human engineers arrived at a similar solution to the same problem,” said IU Bloomington biologist Daniel Kearns, who led the project. “How do you temporarily stop a motor once it gets going?”
The action of the protein they discovered, EpsE, is very similar to that of a car clutch. In cars, the clutch controls whether a car’s engine is connected to the parts that spin its wheels.
We are actually using the knowledge about our own designed artifacts to shed light on biology and how it works. Imagine if there were no computers, tape recorders, and washing machines. Take away human technology, and suddenly, there are no good metaphors left to describe life. - p 52
All of this, of course, makes sense if life really is carbon-based nanotechnology. To understand an alien technology, we would have to use our own technology as a model, and the more similar the technologies, the more easily we could characterize and understand this alien technology. - p 53
If living processes are the products of design, it comes as no surprise that so much of biology is more akin to the study of engineering than to chemistry or physics. Furthermore, it would make sense that as our understanding of the cell advances, that teleological concepts, including the very concept of design, would proliferate in the biological literature. Much of this design terminology stems from the fact that biologists have discovered that cells are filled with miniature machines and that coded information is stored and employed for the synthesis of these machines.- p. 59
Looking at a cell is like looking into the future of our own designs. – p. 204
“Wordle is a toy for generating “word clouds” from text that you provide. The clouds give greater prominence to words that appear more frequently in the source text.”
Here is a Wordle of Chapter 6 from The Design Martrix:
Evidence, evidence, evidence. Lots of people like to use this ill-defined and subjective concept to score points, as it allows people to sit in judgment, pronouncing whether or not some data are “evidence” or whether the evidence is “sufficient.” It’s quite the power-trip to sit in judgment not only of other people, but of Reality. Despite these problems, we cannot ignore the importance of evidence. For example, if we are to convict Jones for the murder of Smith, there had better be evidence to support this contention if we are going to take away Jones’s freedom.
Yet this very example serves to make both points. Yes, evidence is important when making decisions about our natural and social world, but relying solely on the evidence may very well deliver only a superficial, or even false, understanding of the world. We know this simply from the fact that in court rooms around the world, judges and juries have followed the evidence before them to determine guilty people are innocent and innocent people are guilty. This holds true even if we rule out corruption and biases.
Consider some movie where you, the viewer, know that Jones killed Smith, because you watched it happen. Jones, of course, subjectively knows that he killed Smith. The police investigator doesn’t know this, he simply believes that Jones killed Smith because of some clues. The investigator then privately confronts Jones and accuses him of murder. Jones, privately knowing the investigator is correct, simply replies, “There is no evidence and you can’t prove it” and the investigator knows this is true.
Right there, in that scene, we see the difference between evidence and truth. Relying solely on the evidence may very well deliver only a superficial, or even false, understanding of the world.
Jacques Monod shared a Nobel Prize for his work on the lac operon. . This work played a crucial role in the development of molecular biology and ultimately led to the birth of evo-devo. In 1971, Monod wrote a classic book entitled, Chance and Necessity. It begins as follows:
To make a protein, we simply covalently link individual amino acids together via a peptide bond. The figure below shows the formation of a peptide bond.
I’d like to draw your attention to two things. First, note that the carboxyl group of one amino acid reacts with the amino group of the second amino acid to form the peptide bond (highlighted in the orange box). This creates a dipeptide with differing ends. At the N-terminal end, there is a free amino group and the C-terminal end has a free carboxyl group. This simply means we can attached a third amino acid to the C-terminal end of the dipeptide with the very same reaction. And if we can add a third, we can add a fourth. Etc. Thus, the structure of the amino acid is perfectly poised to create a growing chain whose length would be determined by factors other than amino acid structure. We can thus begin to catch a glimpse of one reason why proteins are so versatile, as the relative ease of construction is coupled to an ability to vary the length.
Since we have been talking about proteins, let’s back up to say a few things about their building blocks – the amino acids. Below is a figure of an amino acid.
Note the central carbon atom and how it is covalently bonded with four different groups. Three of these four groups are always the same in every amino acid used by life: the amino group (orange box), the carboxyl group (blue box), and the hydrogen atom. The R signifies the side chain, which differs for each amino acid.
Let me summarize some of the observations I have made with my recent focus on proteins and their role in the success of evolution. Consider the following:
To what degree is the design of a designer constrained by his/her building material? For example, imagine that we enlisted the service of the worlds most creative and brilliant engineers and tasked them to design a space craft that will carry men to Mars and back. Now, let’s add one constraint – the only material available to the designers is concrete. Would these brilliant designers be able to meet the design objective?
Below if a nice video about our modern understanding of evolution.
I especially enjoyed the comments from Sean Carroll (according to Michael Ruse, “Of all the scientists in the world today, there is no one with whom Charles Darwin would rather spend an evening than Sean Carroll.”):
So what this means is in some ways, some sense, evolution is a simpler process than we first thought. When you think about all of the diversity of forms out there, we first believed this would involve all sorts of novel creations, starting from scratch, again and again and again. We now understand that, no, that evolution works with packets of information and uses them in a new and different ways, and new and different combinations, without necessarily having to invent anything fundamentally new, but new combinations.
My, that’s a pretty radical change in the way we view evolution. The old way was far less friendly to teleology and also failed to prepare scientists for the more accurate understanding of evolution, an understanding that is now much more friendly to teleology.
This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?
The vast and immense Tree of Life is a protein-dependent output. Point to
some evidence of evolution and I’ll point to the proteins that underlie it.
Without proteins, would there be a Tree of Life 3.5 billion years after the
RNA world took root? How do we know? If we believe so, would the Tree be
as immense and vast as it is today? A life form composed of nucleic acids,
carbohydrates, and lipids would suffice for the purposes of the blind
watchmaker. But could the blind watchmaker turn this material into
something that is analogous to an Ash tree filled with squirrels, beetles,
and birds?
June 24th, 2008 by 
Mike Gene 
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