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Digital Counters Discovered Controlling Gene Expression


Yet another parallel with human-engineered systems is discovered in the living cell – digital counters that control the number of protein molecules expressed. The researchers obviously aren’t electronic engineers as this particular circuit isn’t analogous to a clock. It’s a counter circuit. It counts from zero to a preset maximum number of operations then stops when the maximum count is reached. This is a very common function employed in digital electronic devices often implemented with what’s called a serial shift register. The shift register starts out containing all zeros. One bits are fed into the input and zeros shift out the other end like putting marbles into an empty tube. When the shift register is full then ones start coming out the other end. Some action is taken when the first one bit emerges at the output. Shift registers can have any arbitrary number of bits.

Isn’t it fascinating how many things conceived by intelligent human designers are found in the molecular machinery of living cells? But hey, ignore the man behind the curtain. Nothing to see here. Click your heels together three times while repeating “It’s all just chance & necessity!” 🙄

Clocking In And Out Of Gene Expression

Source: Baylor College of Medicine
Date: June 15, 2007

Science Daily — A chemical signal acts as time clock in the expression of genes controlled by a master gene called a coactivator, said Baylor College of Medicine researchers in a report that recently appeared in the journal Cell.

“We have long known that our bodies live by a daily and monthly and even yearly clock and that cells have clocks as well,” said Dr. Bert O’Malley, chair of molecular and cellular biology at BCM and senior author of this report. “We have actually taken this concept to the gene now and said that we are made up of 25,000 genes that have clocks too.” Genes get expressed and carry out their functions through proteins, he said. Gene expression involves the machinery of the cell translating the gene’s code into a protein that carries out function. This process has to have a beginning and an end.

“That sets the time clock,” said O’Malley. “The question is, ‘How is this done”‘” The answer lies in coactivators — master genes that turn other genes on and off.

“Inherent to the structure of these coactivators is a clock,” he said. “But the clock needs to be set off.” In studies of breast cancer cells, O’Malley and his colleagues showed how the clock works. Using steroid receptor coactivator-3 (SRC-3), they demonstrated that activation requires addition of a phosphate molecule to the protein at one spot and addition of an ubiquitin molecule at another point. Each time the message of the gene is transcribed into a protein, another ubiquitin molecule is chained on. Five ubiquitins in the chain and the protein is automatically destroyed.

“It’s built-in self destruction,” said O’Malley. “It prevents you from activating a potent factor in the cells that just keeps the clock running and the gene continuing to be expressed.” In that scenario, the result could be cancer, too much growth or an abnormal function.

“It means there’s a fixed length of time that the molecule can work. When it’s activated, it’s already preprogrammed to be destroyed. The clock’s running and each time an ubiquitin is added, it is another tick of the clock.” When the clock system fails, problems result.

“If you can’t start the clock, you can’t stop the clock. If you stop the clock before you should or if it is running too slow or too fast, it causes problems in the cells,” he said.

Others who took part in this work included Drs. Ray-Chang Wu, Qin Feng and David M. Lonard, all of BCM’s department of molecular and cellular biology.

Funding for this research came from the Welch Foundation and the National Institute of Child Health and Human Development and the Nuclear Receptor Signaling Atlas of the National Institute of Diabetes and Digestive and Kidney Diseases.

Note: This story has been adapted from a news release issued by Baylor College of Medicine.

Apparently the type of "programming" involved in protein assembly isn't anything you'd want to show your boss if you were a software engineer: "[O]ne can still understand gene transcription in terms of parallel threads of execution, with the caveat that these threads do not follow canonical, modular subroutine structure. Rather, threads of execution are intertwined in a rather 'higgledy-piggledy' fashion, very much like what would be described as a sloppy, unstructured computer program code with lots of GOTO statements zipping in and out of loops and other constructs." See http://www.genome.org/cgi/content/full/17/6/669 . Jud
CJYman: "I’m wondering if you know of any examples of logic gates used within life." It seems that a lot of the protein nanomachine assembly processes in the cell resemble production assembly control programs, with each step triggered by completion of the previous, all subject to additional feedback regulation. This isn't in the form of a central digital computer and conventional software, but it is equivalent just the same. It is more like massive numbers of digital logic gates distributed throughout the cell, all designed to coordinate with each other in carrying out life processes. Having been reading Edge of Evolution I found several descriptions of these sort of systems, like the assembly of the flagellum on pages 265-267. magnan
DaveScot, Excellent. Thx. CJYman
#12 Borne I've found in your description EXACTLY what has been so far my experience of speaking in favour of ID with NDE supporters. I am more and more sure that it's not possible a fair discussion about. You said: "That’s one of the reasons why they cannot win in this controversy." I think they are realizing that they could lose in the future. kairos
CJYman I’m wondering if you know of any examples of logic gates used within life. Yes. In fact one example was blogged here by Dembski in March of 2006. DaveScot
kairos: From what I can gather from looking at Darwinist forums and books - math, logic and information systems are no where near the studies of bio majors in North Am. It's like no one has woke up yet to the fact that bio information systems are uncannily similar (but far more advanced) to our own info systems. Look at any debate forum on evo vs ID. It's always the same. The logic of Darwinists is appalling and their understanding of information systems is even worse - even amongst the computer science people among. Just considering the present subject - how will they attempt to squirm out of the most obvious explanation? We all know the answer. It doesn't seem to matter to them how many such complex, obviously designed with a purpose, systems are found in living cells - their preconceived metaphysical concepts bring them to denial, hand waving and yet another just-so story or 2 or 3. They never stop to really think about what they "believe" - just spew out whatever inane nonsense seems to come to their rescue of their precious theory in their minds. They commit the same logical fallacies over and over ad infinitum ad nauseum But never see it. And you can't tell them! The responses are always the same - denial, insults, hand waving, double talk, just so stories and elephant hurling. Anything to get away from the truth. The simplest reasoning escapes them. Which is why I've come to the conclusion over the years that Darwinists/Atheists are immune to logic - it means nothing to them - they cannot see the obvious or reason out the simplest statements. That's one of the reasons why they cannot win in this controversy. Borne
I would ask a (perhaps unpolitically correct question). In my european experience the undergraduate students in the biological academic courses show very low attitudes for maths and computer sciences. The question is: is so in the USA too? If this should be the case perhaps we haven't to be much surprised about the fact that probabilistic arguments are largely not understood by NDE biologists :-) kairos
This sounds like the ID movement needs to campaign for “Digital Electronics for all” in the HS and introductory level College curriculum! (Time to end the dominance of IT training by user-interface manipulation and software-oriented instruction? At least, this would create a mass-base for understanding what design thinkers are thinking about . . .)
At least anyone getting a Ph.D. in biology needs to have a foundation in digital electronics. It shouldn't take these guys too long to see the parallels. Maybe they'll show us how to design more elaborate of electronic circuits by RM+NS. bFast
I guess it would be the supression of some type of timing logic that would enable lactase persistance. bornagain77
Hello Dave, I'm wondering if you know of any examples of logic gates used within life. CJYman
Dave & Gil: Digital counter-controlled molecular level life systems to get phase co-ordination, synchronisation and control and thus prevent runaway or no-start hazards? (And, at Baylor . . . .?) Add that to DNA-based digital codes for protein syntehsis, discrete state controlled gene expression, underlying algorithms and the like. This sounds like the ID movement needs to campaign for "Digital Electronics for all" in the HS and introductory level College curriculum! (Time to end the dominance of IT training by user-interface manipulation and software-oriented instruction? At least, this would create a mass-base for understanding what design thinkers are thinking about . . .) Sooner or later, given the accelerating digitalisation of the culture, some ideas are going to click into a new configuration and the paradigm will shift dramatically across the community then the academy, leaving the "chance is god" holdouts culturally isolated. The next 10 - 20 years are going to be very interesting . . . GEM of TKI kairosfocus
Just this week I've been pulling my hair out at work trying to resolve timing and counter issues between multiple interacting software and hardware systems: an embedded system with a slow CPU and two types of memory that run at different speeds, flash and SRAM; a fast ethernet connection communicating wirelessly; and a PC running at high speed but with slow disk I/O compared to other components of the integrated system. The final issues were solved today. Interestingly enough, trial and error played a role in the problem-solving process, but the trials were focused, and information gleaned from the errors provided insight as to how to modify the system, in multiple ways and simultaneously, so that the interacting parts could communicate coherently. Dudes like Coyne should be required to solve problems like this before they shoot their mouths off about the power of natural selection. I'm going to play some Chopin on my piano now, for therapeutic purposes. GilDodgen
I've been wating for something like this to be discovered for a very long time. Further, I bet that as the evidence is gathered, it is in these timer/counter systems that random mutation can truly take a useful role. bFast
To explain all this we must invoke our old friend "The Blind Watchmaker". idnet.com.au
The web reference for this is http://www.sciencedaily.com/releases/2007/06/070614121506.htm idnet.com.au
I wonder how much more of this stuff it will take before the chance worshipers realize that the object of their worship is a false god. GilDodgen
Hey Dave could you or someone who knows the issue better than I, post a rebuttal here "http://newtonsbinomium.blogspot.com/2006/10/ review-of-mystery-of-genome-ii.html" It would be great to see him squirm. heyman

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