Genetic on/off Switches

[bob b]

The Genetic On-Off Switch
by Stephen Caesar
06/21/2006
Many times in previous installations of this column I have referred to the genetic on-off switch, an amazing creation pre-programmed into the genetic code of all living things which, when triggered by external environmental stimuli, causes sudden changes in the individual creature. These changes are sometimes so radical that scientists have mistakenly identified them as examples of evolution via natural selection and survival of the fittest.
___These on/off switches are mysterious proteins known as transcription factors, and scientific research has shown that these proteins are an integral, pre-set part of the genome, the genetic structure of every living being. According to Dr. Martha Bulyk, who is investigating the phenomenon of genetic on/off switches, “We get such complex life forms and processes and all the instructions are included in the genome somehow” (Powell 2005: 3).
___Bulyk, assistant professor of medicine, pathology, health sciences, and technology at Harvard Medical School, is a pioneer in the use of microarray technology in the scientific analysis of transcription factors. Her most recent work in this field, published in the December 2004 issue of the journal Nature Genetics, earned her recognition from the Massachusetts Institute of Technology’s Technology Review magazine, which listed her among the top 35 technology innovators under age 35 (Ibid.).
___Science has known for a long time now that the blueprint of life is contained in DNA, which consists of long, double-stranded helical molecules in the nucleus of every cell in every living creature on Earth. The DNA helix itself is comprised of a series of base pairs, the order of which determines every single physical aspect of any living being. The DNA is put into action through a process known as transcription, by which a special enzyme breaks apart the DNA helix, reads the genetic code pre-programmed into the blueprint of every living creature, and then creates an RNA molecule that in turn carries that code to another location in the cell to be translated into action. Proteins that bind to specific DNA regulatory elements regulate this transaction process. These regulatory proteins are Bulyk’s transcription factors (Ibid.).
___As has been discussed many times in this column, scientists have witnessed firsthand these transcription factors or “on/off switches” being engaged, usually by external factors such as radical, often catastrophic, environmental changes. The changes in an individual species brought about by the turning on (or off) of these transcription proteins are sometimes so profound that the species in question often appears to transform into a completely new species. However, this is not trans-specific macroevolution via random mutation and consequent survival of the fittest, as Darwin had theorized.
___Instead, the on-off switches show all the appearance, as mentioned above, of having been pre-programmed into the blueprint of every living creature on the planet. It is almost as if someone intentionally did this so that all living things would be able to survive and overcome the uncountable disasters, environmental changes, and radical transformations the world would undergo in its long history.

Reference: Powell, A. 2005. “Bulyk searches for DNA on-off switches.” Harvard Gazette, Nov. 3.

 

[MindonFire]

subtraction of quote

subtraction of quote

Could these switches be used to grow and regenerate limbs and lost organs?

 

[bob b]

Could these switches be used to grow and regenerate limbs and lost organs?

I would be willing to bet that in the future someone will try to do so.

I did see a program once on PBS in which they had successfully grown what looked like a human ear on the back of a mouse. I don't even want to think about what might come in the next hundred years.

"Stop the World, I want to get off".

 

[Evoken]

As has been discussed many times in this column, scientists have witnessed firsthand these transcription factors or “on/off switches” being engaged, usually by external factors such as radical, often catastrophic, environmental changes. The changes in an individual species brought about by the turning on (or off) of these transcription proteins are sometimes so profound that the species in question often appears to transform into a completely new species. However, this is not trans-specific macroevolution via random mutation and consequent survival of the fittest, as Darwin had theorized.

I don't see why not. That seems to actually make it easier for macroevolution to occur and to increase the rate too.

The on/off genes are called "Hox genes" i believe. I think I saw a paper somewhere dealing with them and their evolution, I will post the link when I find it.

EDIT.. Found it on a thread I had started last year on IIDB. The post contains a couple of links dealing with them...
http://iidb.org/vbb/showthread.php?p=2808268#post2808268


Valz

 

[CapnFungi]

If its pre programmed it can't be random. That is why not.

 

[bob b]

Hox (Homeobox) Genes Evolution’s Saviour?
© 2000 Don Batten, Ph.D.. All Rights Reserved. [Last Modified: 09 March 2006]

Some evolutionists hailed homeobox or hox genes as the saviour of evolution soon after they were discovered. They seemed to fit into the Gouldian mode of evolution (punctuated equilibrium) because a small mutation in a hox gene could have profound effects on an organism. However, further research has not born out the evolutionists’ hopes. Dr Christian Schwabe, the non-creationist sceptic of Darwinian evolution from the Medical University of South Carolina (Dept. of Biochemistry and Molecular Biology), wrote:

Control genes like homeotic genes may be the target of mutations that would conceivably change phenotypes, but one must remember that, the more central one makes changes in a complex system, the more severe the peripheral consequences become. … Homeotic changes induced in Drosophila genes have led only to monstrosities, and most experimenters do not expect to see a bee arise from their Drosophila constructs.’ (Mini Review: Schwabe, C., 1994. Theoretical limitations of molecular phylogenetics and the evolution of relaxins. Comp. Biochem. Physiol. 107B:167–177).

Research in the six years since Schwabe wrote this has only born out his statement. Changes to homeotic genes cause monstrosities (two heads, a leg where an eye should be, etc.); they do not change an amphibian into a reptile, for example. And the mutations do not add any information, they just cause existing information to be mis-directed to produce a fruit-fly leg on the fruit-fly head instead of on the correct body segment, for example.

Evolutionists, of course, use the ubiquity of hox genes in their argument for common ancestry (‘Look, all these creatures share these genes, so all creatures must have had a common ancestor’). However, commonality of such features is to be expected with their origin from the same (supremely) intelligent Creator. All such homology arguments are only arguments for evolution when one excludes, a priori, origins by design. Indeed many of the patterns we see do not fit common ancestry. For example, the discontinuity of distribution of hemoglobin-like proteins, which are found in a few bacteria, molluscs, insects, and vertebrates. One could also note features such as vivipary, thermoregulation (some fish and mammals), eye designs, etc.

 

[Evoken]

Evolutionists, of course, use the ubiquity of hox genes in their argument for common ancestry (‘Look, all these creatures share these genes, so all creatures must have had a common ancestor’). However, commonality of such features is to be expected with their origin from the same (supremely) intelligent Creator.

The inference of common descent is based on much more than just mere similarities. This is a common misunderstanding on the part of Evolution critics.

Now, I do not see how the inference of common descent and the inference of a common designer are mutually exclusive.


Valz

 

[MindonFire]

So, what exactly do these switches switch on or off?


Could this be what is meant in 1 John 3:2 Beloved, now are we the sons of God, and it doth not yet appear what we shall be: but we know that, when he shall appear, we shall be like him; for we shall see him as he is.

Transmute: (vrb) transitive verb 1 : to change or alter in form, appearance, or nature and especially to a higher form 2 : to subject (as an element) to transmutationintransitive verb : to undergo transmutation
synonyms see TRANSFORM

 

[Johnny]

The on/off genes are called "Hox genes" i believe. I think I saw a paper somewhere dealing with them and their evolution, I will post the link when I find it.

"On/off genes" are a reference to transcription factors (promoters, enhancers), repressors, and inducers.

 

[bob b]

The inference of common descent is based on much more than just mere similarities. This is a common misunderstanding on the part of Evolution critics.

I await enlightenment.

Now, I do not see how the inference of common descent and the inference of a common designer are mutually exclusive.
Valz

There is no question that common descent occurs. For example, both evolutionists and creationists believe that all humans living today descended from a single female as well as a single male only thousands of years ago. This was demonstrated by DNA studies.

But similar DNA studies that show how closely related all humans are, when applied to other animals, show vast DNA differences separating the major types, something not predicted by evolutionary theory. Thus, punctuated equilibria was postulated to fix the problem.

If one assumes that only a few DNA changes are needed to make a great difference in morphology, thus "fixing" the problem with the fossil record having no evidence of major morphological changes between types, because they happened too fast to be preserved, it unfortunately makes the DNA problem worse, because the DNA evidence shows that major DNA changes had to have occurred between the major types to explain the vast DNA differences between major types.

Heads creationists win, tails evolutionists lose.

 

[Johnny]

show vast DNA differences separating the major types, something not predicted by evolutionary theory.

What are you talking about "vast DNA differences"? Did you know that humans and mice share 99% of the same genes, of which share 85% sequence homology? For organisms so far apart, that's really strikingly similar. Secondly, DNA differences are expected to increase in direct proportion to evolutionary distance. Humans and jawless fish are quite far apart, and so evolutionary theory predicts that our genomes will be more different then humans and chimps, or humans and mice even.

Thus, punctuated equilibria was postulated to fix the problem.

That's not why punctuated equilibria was postulated. You know that.

because the DNA evidence shows that major DNA changes had to have occurred between the major types to explain the vast DNA differences between major types.

Maybe you should study the topic, find some examples, and then get back to us. Anyone can make stuff up.

You're getting sloppy. The post you just made can be described as nothing other than creationist disinformation. This is what we speak of when we talk of creationist nonsense. It sounds scientific, but it's just plain wrong! This is what happens when your working knowledge of biology comes from creationist tracks and material. This is the very reason I'm so discontent with the creationist community. It appears you had absolutely no moral problem posting this. Afterall you can always appeal to ignorance or silence when you're called out on this (judging by the past, it will be the latter). But someone with a foundation in biology could never, in good conscience, post something like this.

 

[bob b]

What are you talking about "vast DNA differences"? Did you know that humans and mice share 99% of the same genes, of which share 85% sequence homology? For organisms so far apart, that's really strikingly similar. Secondly, DNA differences are expected to increase in direct proportion to evolutionary distance. Humans and jawless fish are quite far apart, and so evolutionary theory predicts that our genomes will be more different then humans and chimps, or humans and mice even.
That's not why punctuated equilibria was postulated. You know that.Maybe you should study the topic, find some examples, and then get back to us. Anyone can make stuff up.

You're getting sloppy. The post you just made can be described as nothing other than creationist disinformation. This is what we speak of when we talk of creationist nonsense. It sounds scientific, but it's just plain wrong! This is what happens when your working knowledge of biology comes from creationist tracks and material. This is the very reason I'm so discontent with the creationist community. It appears you had absolutely no moral problem posting this. Afterall you can always appeal to ignorance or silence when you're called out on this (judging by the past, it will be the latter). But someone with a foundation in biology could never, in good conscience, post something like this.

Ah, but you are sloppy in saying that a person with a foundation in biology would never say (or post) this, because I get my information from what they have said.

 

[Evoken]

I await enlightenment.

"The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity."

From 29+ Evidences for Macroevolution. That entire essay is nothing but an exposition of all the things that are considered as evidence and they go beyond mere similarity.

Likewise this article says...

"Consider first how evolutionists interpret similarities between species living today. Present-day humans and chimpanzees, despite obvious external and behavioral differences, have extremely similar internal organs and physiological functions; indeed their genes are more than 98% identical (Goodman et al., J Molec Evolution 30:260,1990). Just as the resemblance between two siblings suggests a common parentage, resemblance between species suggests common ancestors.

Species less similar to humans than are apes--mice, for example--are believed to have branched off millions of years earlier from a common primitive mammalian ancestor. Evolutionary family tree diagrams that express such relationships between species have been constructed by evolutionary biologists by analyzing similarities of present-day organisms.

Another extensive source of data that has been of major importance in constructing similarity tree diagrams is the species comparison of proteins and genes."

That article also goes to great lenghts to show that not only the things that work but also those that do not (pseudogenes) are similar among species.


Valz

 

[Evoken]

If its pre programmed it can't be random. That is why not.

Sure, but that doesn't means that they could not have come about via natural processes. Such as Natural Selection and Random Mutations. The word "random" by the way has a different meaning in a scientific context than it does in an ordinary day context. Evolution is not random in the ordinary day context.

See here, look for the point "The theory of evolution says that life originated, and evolution proceeds, by random chance"...

http://talkorigins.org/faqs/faq-misconceptions.html


Valz

 

[bob b]

"The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern produced by a branching evolutionary process, such as common descent, is much more specific than simple similarity."

From 29+ Evidences for Macroevolution. That entire essay is nothing but an exposition of all the things that are considered as evidence and they go beyond mere similarity.

Likewise this article says...

"Consider first how evolutionists interpret similarities between species living today. Present-day humans and chimpanzees, despite obvious external and behavioral differences, have extremely similar internal organs and physiological functions; indeed their genes are more than 98% identical (Goodman et al., J Molec Evolution 30:260,1990). Just as the resemblance between two siblings suggests a common parentage, resemblance between species suggests common ancestors.

Species less similar to humans than are apes--mice, for example--are believed to have branched off millions of years earlier from a common primitive mammalian ancestor. Evolutionary family tree diagrams that express such relationships between species have been constructed by evolutionary biologists by analyzing similarities of present-day organisms.

Another extensive source of data that has been of major importance in constructing similarity tree diagrams is the species comparison of proteins and genes."

That article also goes to great lenghts to show that not only the things that work but also those that do not (pseudogenes) are similar among species.


Valz

Evidence has come to light since your article was written that "pseudogenes" do have an important function even though they do not code for proteins.

In addition it is always best to read "the other side" before forming an opinion. For example, over the years I have managed to read most if not all of the articles at talk.origin and other atheistic websites.

http://www.trueorigin.org/theobald1a.asp

BTW, we recognize that evolutionists do not say that life proceeds by random chance but they do claim it proceeds by random mutations. They then try to convince us that by eliminating all the failures the process will produce more and more complex and sophisticated offspring. This ignores the fact that each offspring contains multiple mutations, dozens if not hundreds more mutations in its genome than its parents did, and hence it is inevitable than each generation is accumulating mutations in its genome. Since unfavorable mutations far unnumber favorable ones the best that natural selection can do is to kill off the worst of the offspring, leaving offspring that are admittedly the best of the offspring, but are still slightly worst off than the parents.

If one starts with perfect genomes, the error correction machinery and the redundant and "fail soft" nature of the design, coupled with a natural selection that kills off the worst cases, populations can hold off the inevitable for some time, perhaps a few hundred generations or so in the case of mankind.

But the very long term outlook, extinction, is never in doubt.

 

[Johnny]

Ah, but you are sloppy in saying that a person with a foundation in biology would never say (or post) this, because I get my information from what they have said.

Then doesn't that say something about the integrity of your sources? I want sources for these three claims. I suspect you added your own little flavor to what was said. Cite URLs, papers, anything. I want to see the credentials of the inept biologist who is making these claims. Claim #1 is demonstrably false. Claim #2 is just outright wrong. Claim #3 is questionable. I'd like to see how the author supports this contention.

Claim #1: "But similar DNA studies that show how closely related all humans are, when applied to other animals, show vast DNA differences separating the major types, something not predicted by evolutionary theory."
Claim #2: "Thus, punctuated equilibria was postulated to fix the problem."
Claim #3: "because the DNA evidence shows that major DNA changes had to have occurred between the major types to explain the vast DNA differences between major types."

 

[bob b]

Then doesn't that say something about the integrity of your sources? I want sources for these three claims. I suspect you added your own little flavor to what was said. Cite URLs, papers, anything. I want to see the credentials of the inept biologist who is making these claims. Claim #1 is demonstrably false. Claim #2 is just outright wrong. Claim #3 is questionable. I'd like to see how the author supports this contention.

Claim #1: "But similar DNA studies that show how closely related all humans are, when applied to other animals, show vast DNA differences separating the major types, something not predicted by evolutionary theory."
Claim #2: "Thus, punctuated equilibria was postulated to fix the problem."
Claim #3: "because the DNA evidence shows that major DNA changes had to have occurred between the major types to explain the vast DNA differences between major types."

Since you are the one so incensed that I am wrong, instead of asking me to take your word for it why not prove me wrong?

 

[Johnny]

Since you are the one so incensed that I am wrong, instead of asking me to take your word for it why not prove me wrong?

Let me see your sources. The discussion will continue when I've read your sources.

 

[bob b]

Let me see your sources. The discussion will continue when I've read your sources.

No, it will continue when you give your evidences that I was wrong. (I love to counterpunch).

 

[Johnny]

No, it will continue when you give your evidences that I was wrong. (I love to counterpunch).

So you pass off the blame on your sources, and then you refuse to divulge them. How amusing. All I'm asking for is your sources. I am not asking you to defend them. I just want to read the sources for myself.

(I love to counterpunch).

That's not a counter-punch. That's called taking the heat off yourself by passing it back to me.

Where are your sources? Do you even have them?