A software engineer on convergent evolution

_{Denyse O'Leary

September 7, 2013

Convergent evolution}

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Further to “Convergent evolution seen in 100s of genes,”

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me. …

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

High rates of convergent evolution are only “incredible” if we simply assume as an article of faith that there is no design, and that therefore there is nothing to research. It shall remain then, forever, incredible. No matter why the design exists.

A price paid, shall we say, for dogmatism killing curiosity.

Comments

High rates of convergent evolution are only “incredible” if we simply assume as an article of faith that there is no design, and that therefore there is nothing to research. It shall remain then, forever, incredible. No matter why the design exists. A price paid, shall we say, for dogmatism killing curiosity.
Except it's not an article of faith. Aside from all the evidence that can be explained by common descent with modification science prefers to NOT assume causes unless they're necessary. And it has not been proven that an undefined and undetected designer whose abilities and time frame are not specified is necessary. And to claim at this point that Design is a better explanation than modern evolutionary theory because it has not been proven that evolutionary theory can 'do the job' is trying to prove a negative with an argument of incredulity. Also, it's extremely disingenuous to say that there is no research going on regarding convergent evolution. It's all very well and good to preach to the choir but that doesn't excuse getting the message wrong. As far as dogma killing curiousity . . . which field is generating more research: ID or modern evolutionary theory?Jerad_{September 7, 2013
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Thanks Querius.Collin_{September 7, 2013
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Collin, Ansel Adams once stated that everything interesting happens at the edges. One of those edges in Biology is the platypus, a biological version of Frankenstein's monster. Apparently, its genome is as much of a patchwork as its appearance. This discovery lends some credence to the idea of "bristle block" DNA, where instead of tiny changes over time, large chunks of DNA are somehow transferred between different organisms, perhaps through viruses. On the other hand, epigenetics pretty much throws a monkey wrench into all these theories.Querius_{September 7, 2013
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not calling anyone here a new atheist,,but I find it strange that when atheists argue against the omnipotence of God, they usually try to use logical contradictions and never pause to consider that they themselves cannot even create a single photon from their own thought, much less an entire universe.,, A few notes along that line,, a ‘uncollapsed’ photon, in its quantum wave state, is mathematically defined as ‘infinite’ information:
Wave function Excerpt "wave functions form an abstract vector space",,, This vector space is infinite-dimensional, because there is no finite set of functions which can be added together in various combinations to create every possible function. http://en.wikipedia.org/wiki/Wave_function#Wave_functions_as_an_abstract_vector_space Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) http://www.cas.umt.edu/phil/faculty/duwell/DuwellPSA2K.pdf Quantum Computing – Stanford Encyclopedia Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,, http://plato.stanford.edu/entries/qt-quantcomp/#2.1
Thus every time we see (observe) a single photon of ‘material’ reality we are actually seeing just a single bit of information that was originally created from a very specific set of infinite information that was known by the consciousness that preceded material reality. i.e. information known only by the infinite Mind of omniscient God!
Job 38:19-20 “What is the way to the abode of light? And where does darkness reside? Can you take them to their places? Do you know the paths to their dwellings?” “When I consider what marvelous things men have understood, what he has inquired into and contrived, I know only too clearly that the human mind is a work of God, and one of the most excellent.” Yet the potential of the human mind “… is separated from the Divine knowledge by an infinite interval.” (Poupard, Cardinal Paul. Galileo Galilei. Pittsburgh: Duquesne University Press, 1983, p. 101.)
Besides photons, even space-time itself renders proof towards the omniscience/omnipotence of God:
“It always bothers me that in spite of all this local business, what goes on in a tiny, no matter how tiny, region of space, and no matter how tiny a region of time, according to laws as we understand them today, it takes a computing machine an infinite number of logical operations to figure out. Now how can all that be going on in that tiny space? Why should it take an infinite amount of logic to figure out what one stinky tiny bit of space-time is going to do?" - Richard Feynman – one of the founding fathers of QED (Quantum Electrodynamics) Quote taken from the 6:45 minute mark of the following video: https://www.youtube.com/watch?v=obCjODeoLVw THE INFINITY PUZZLE: Quantum Field Theory and the Hunt for an Orderly Universe Excerpt: In quantum electrodynamics, which applies quantum mechanics to the electromagnetic field and its interactions with matter, the equations led to infinite results for the self-energy or mass of the electron. After nearly two decades of effort, this problem was solved after World War II by a procedure called renormalization, in which the infinities are rolled up into the electron’s observed mass and charge, and are thereafter conveniently ignored. Richard Feynman, who shared the 1965 Nobel Prize with Julian Schwinger and Sin-Itiro Tomonaga for this breakthrough, referred to this sleight of hand as “brushing infinity under the rug.” http://www.americanscientist.org/bookshelf/pub/tackling-infinity
I don’t know about Feynman, but as for myself, being a Christian Theist, I find it rather comforting to know that it takes an ‘infinite amount of logic to figure out what one stinky tiny bit of space-time is going to do’:
John1:1 "In the beginning was the Word, and the Word was with God, and the Word was God."
of note: ‘the Word’ in John1:1 is translated from ‘Logos’ in Greek. Logos is the root word from which we derive our modern word logic http://etymonline.com/?term=logic supplemental note; As well as the universe having a transcendent beginning, thus confirming the unique Theistic postulation of Genesis 1:1, the following recent discovery of a 'Dark Age' for the early universe uncannily matches up with the Bible passage in Job 38:4-11. For the first 400,000 years of our universe’s expansion, the universe was a seething maelstrom of energy and sub-atomic particles. This maelstrom was so hot, that sub-atomic particles trying to form into atoms would have been blasted apart instantly, and so dense, light could not travel more than a short distance before being absorbed. If you could somehow live long enough to look around in such conditions, you would see nothing but brilliant white light in all directions. When the cosmos was about 400,000 years old, it had cooled to about the temperature of the surface of the sun. The last light from the "Big Bang" shone forth at that time. This "light" is still detectable today as the Cosmic Background Radiation. This 400,000 year old “baby” universe entered into a period of darkness. When the dark age of the universe began, the cosmos was a formless sea of particles. By the time the dark age ended, a couple of hundred million years later, the universe lit up again by the light of some of the galaxies and stars that had been formed during this dark era. It was during the dark age of the universe that the heavier chemical elements necessary for life, carbon, oxygen, nitrogen and most of the rest, were first forged, by nuclear fusion inside the stars, out of the universe’s primordial hydrogen and helium. It was also during this dark period of the universe the great structures of the modern universe were first forged. Super-clusters, of thousands of galaxies stretching across millions of light years, had their foundations laid in the dark age of the universe. During this time the infamous “missing dark matter”, was exerting more gravity in some areas than in other areas; drawing in hydrogen and helium gas, causing the formation of mega-stars. These mega-stars were massive, weighing in at 20 to more than 100 times the mass of the sun. The crushing pressure at their cores made them burn through their fuel in only a million years. It was here, in these short lived mega-stars under these crushing pressures, the chemical elements necessary for life were first forged out of the hydrogen and helium. The reason astronomers can’t see the light from these first mega-stars, during this dark era of the universe’s early history, is because the mega-stars were shrouded in thick clouds of hydrogen and helium gas. These thick clouds prevented the mega-stars from spreading their light through the cosmos as they forged the elements necessary for future life to exist on earth. After about 200 million years, the end of the dark age came to the cosmos. The universe was finally expansive enough to allow the dispersion of the thick hydrogen and helium “clouds”. With the continued expansion of the universe, the light, of normal stars and dwarf galaxies, was finally able to shine through the thick clouds of hydrogen and helium gas, bringing the dark age to a close. (How The Stars Were Born - Michael D. Lemonick) http://www.time.com/time/magazine/article/0,9171,1376229-2,00.html
Job 38:4-11 “Where were you when I laid the foundations of the earth? Tell me if you have understanding. Who determined its measurements? Surely you know! Or who stretched a line upon it? To what were its foundations fastened? Or who laid its cornerstone, When the morning stars sang together, and all the sons of God shouted for joy? Or who shut in the sea with doors, when it burst forth and issued from the womb; When I made the clouds its garment, and thick darkness its swaddling band; When I fixed my limit for it, and set bars and doors; When I said, ‘This far you may come but no farther, and here your proud waves must stop!" Hidden Treasures in the Book of Job - video http://www.youtube.com/watch?v=7sl0Ln3Ptb8
Music:
Michael W. Smith - Agnus Dei http://www.youtube.com/watch?v=HPBmFwBSGb0
bornagain77_{September 7, 2013
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@Mapou 12
Omnipotence is a flawed concept simply because it leads to an infinite regress
Only if you presume a naive definition of omnipotence. Very few theists would claim that being omnipotent means that God could do logically incoherent things.LT_{September 7, 2013
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kairosfocus @11:
But, in phil and theol, the blanket claim that omnipotence is flawed is a dubious assertion.
Maybe so but, from my perspective, neither philosophy nor theology is immune to logic. It's the other way around. Omnipotence is a flawed concept simply because it leads to an infinite regress.Mapou_{September 7, 2013
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M, I would suggest that there is no need to get into debates over omnipotence to address issues of inductively grounding reliable signs of design as causal process. But, in phil and theol, the blanket claim that omnipotence is flawed is a dubious assertion. It is subtle and challenging, but that does not mean flawed, any more than the sophistication in ever so many branches of math reflect flaws. KFkairosfocus_{September 7, 2013
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I should add, I heard about but did mot even attempt code interweaving, I rejoiced and gave fervent thanks that we could get affordable 1k x 4 bit RAM and 2k x 8 EPROMs. (I have a neighbour who was of an earlier generation, and when he built an astronomically expensive 1 MB RAM for research on video processing, people literally travelled across a continent just to see it.) If you want a single smoking gun on the DNA code, interweaving is it.kairosfocus_{September 7, 2013
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@ Collin:
But does that mean that the designer is not omnipotent?
Absolutely. Omnipotence is a seriously flawed concept.Mapou_{September 7, 2013
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Although I see the author's intent and it's a good one, I think the analogy is a little on the faulty side. As it turns out, echolocating bats and whales do have a common ancestor, some primitive mammal or other. The problem is that the two species branched out possibly millions of years before almost identical and highly complex gene segments for echolocation appeared in both. Stating that this is highly improbable (incredible) is to miss the point entirely in my opinion. The probability of that happening via natural means is exactly zero. Why? Because the random nature of gene mutations guarantees that the echolocating gene segments would be dissimilar in the two species. All programmers know that there is a huge number of ways to design and code a word processor. Imagine how many ways there are to design and code something as enormously complex as echolocation. Entire neuronal subnetworks with complex sensorimotor programs would have to be designed to handle the generation and interpretation of the signals. It would come as no surprise to me if bats and whales turn out to have identical genetic codes for the neural circuitry, too. Inescapable conclusion from the above: The theory of evolution is soundly falsified.Mapou_{September 7, 2013
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"Also, we do have wings on “rats” . . . we call them bats. KF." Well played. My atheist friend said that whales should have gills because they are much more efficient, but it would take too many millions of years for a mammal to evolve them so it hasn't happened yet. But it doesn't seem like gills could provide very much oxygen for their giant brains. I would like to ask a marine biologist about this. I also know that you can't just plug in a feature into a program or a species. It would be like running Mario Bros on Windows. You have to program an entire emulator device to make it work. And why would a designer do that to a whale when its lungs work just fine? But does that mean that the designer is not omnipotent?Collin_{September 7, 2013
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Also, we do have wings on "rats" . . . we call them bats. KFkairosfocus_{September 7, 2013
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While it is important to note how computer programmers may reuse particular strings of code in different computer programs that don't have a 'common ancestor', (save for the programmer himself) and how that conforms to what is being found in similar sequences of code being found in widely divergent genomes, it is also important to note how these genetic programs differ from humanly designed computer programs, i.e. how much more ingenious genetic codes are in their design. For instance,,,
'It's becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can't even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and More the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.' - Dr. John Sanford - 31 second mark of following video http://www.youtube.com/watch?feature=player_detailpage&v=YemLbrCdM_s#t=31s Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
Of related note is how the engineering in a cell easily surpasses our best humanly engineered systems. For instance here are a few examples that will give a small, i.e. a very small, glimpse of how the engineering in the cell easily surpasses man-made devices,,
Bio-Mechanics - Don't the Intricacy & Ubiquity of Molecular Machines Provide Evidence for Design? by Casey Luskin - Spring 2012 Excerpt:,, biomolecular machines have a major difference that distinguishes them from human technology: their energetic efficiency dwarfs our best accomplishments. One paper observes that molecular machines "are generally more efficient than their macroscale counterparts,"7 and another suggests that the efficiency of the bacterial flagellum "could be ~100%."8 Human engineers can only dream of creating such devices. http://www.salvomag.com/new/articles/salvo20/molecular-machines-evidence-for-design.php Problems with the Metaphor of a Cell as "Machine" - July 2012 Excerpt: Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life. Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others. Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,, - James Barham http://www.evolutionnews.org/2012/07/problems_with_t062691.html DNA - Replication, Wrapping & Mitosis - video (notes in description) http://vimeo.com/33882804 Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
etc.. etc..bornagain77_{September 7, 2013
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As a software developer I can also vouch for this 100%. As for gills on whales I don't think they would be able to provide enough oxygen for such a high metabolism animal.JoeCoder_{September 7, 2013
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But why don’t we find gills on whales or wings on cats?
because they don't have them?cantor_{September 7, 2013
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I think that this is very important and shows signs of design. But why don't we find gills on whales or wings on cats?Collin_{September 7, 2013
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Nicely stated! This is a good example of a paradigm blinding the observer. Easy to do.Querius_{September 7, 2013
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