System upgrades shows hopelessness of Darwinian evolution

In my Part 1 post I asked the question if it is really possible to ‘modify a machine while it is running’ like the evolution story maintains and also requires for it to be even plausible.  I used the troubled upgrade and shutdown of considerthegospel.org to raise the question.

Irreducible complexity & evolution of the Giraffe neck

To continue along this line, think for a minute about the well-known tale of the evolution of the long giraffe neck – a rather trivial ‘modification’ when compared others that must have occurred if this story is true.  The popularized idea is that in times of drought the giraffe ‘ancestors’ (something like a horse) with longer necks could reach leaves higher up in trees, and with this selective pressure, over numerous generations successive giraffes developed longer and longer necks.  The  image below illustrates this account.

Darwin's evolution of giraffe

This illustrates the standard ‘story’ of giraffe evolution whereby with selective pressure the longer necks were more adaptable in times of drought.

It seemed so intuitively obvious that it has become a persuasive icon for the evolution story in the popular culture.  But look again at this story with some scientific skepticism.  The long neck and limbs of the giraffe must work in conjunction with the circulatory system that brings blood to the head.  Because the head is about 2 meters above the heart, the blood pressure produced by the heart is about 2x that of a mammal of comparable weight.  That is just a matter of the physics of fluids.  But if the blood pressure is to be that high then the artery walls must also be stronger or the giraffe will die of internal bleeding.   The neck length, heart pressure and arterial wall strength must all be balanced.  But now think for a moment what happens to the giraffe when he suddenly drops his head to the ground to drink.  Instantaneously the head goes from 2m above the heart to about 2m below the heart.  And now the extra blood pressure of the heart is a liability because the increased pressure in its head would blow its brains out.  The reason that this does not happen is that the giraffe has a special organ in his head, unique to giraffes, called the rete mirabile, that regulates the surge in blood pressure.  Without that organ all the other component adjustments of heart and veins would be useless – it would die every time it lowered its head to drink.
And then when the giraffe raises his head again after his drink it should faint from the blood loss from the brain.  When we stand up suddenly we can sometimes feel dizzy.  This is because as we stand up the blood drains from the brain.  Consider the blood drain on the brain when the head goes rapidly through a 4m elevation change.  What keeps giraffes from regularly fainting after they drink is that they have a unique set of one-way valves that regulates blood drain from the brain.  Without these valves, having all of the rete mirabile, the stronger heart, and the stronger vein walls would all be useless because the giraffe would still regularly faint after his drink.

Structure of giraffe showing what it takes for it to be able to take a drink

The interrelated system of features, organs and modifications that are required just for the giraffe to do a simple thing like take a drink.
From Davis & Kenyon. Of Pandas and People. 1993 p.70

These structures are illustrated in this diagram.  When actually looking ‘under the hood’ at what is required even for a relatively simple modification like the elongation of a neck the evolutionary story rapidly goes from an obvious icon to one that raises lots of questions.  The problem is that very few have bothered to look under the hood.  They preferred a sure-sell story.

Stephen J Gould on the Giraffe Neck

The late Stephen J Gould, well-known Harvard paleontologist had this to say about the giraffe neck story in an article in Natural History. (The Tallest Tale, Natural History v105 p18-23+, 196)

I made a survey of all major high-school textbooks in biology. Every single one — no exceptions — began its chapter on evolution by first discussing Lamarck’s theory of the inheritance of acquired characteristics, and then presenting Darwin’s theory of natural selection as a preferable alternative. All texts then use the same example to illustrate Darwinian superiority — the giraffe’s neck.

In the realm of giraffes, current use of maximal mammalian height for browsing leaves does not prove that the neck evolved for such a function…Why then have we been bamboozled into accepting the usual tale without questioning?

He concludes:

Darwinian evolution may be both true and powerful, but if we continue to illustrate our conviction with an indefensible, unsupported, entirely speculative, and basically rather silly story, then we are clothing a thing of beauty in rags—and we should be ashamed,

So it turns out that the giraffe account, when finally analyzed has turned out to be nothing more than a ‘tale’ that has ‘bamboozled’ us and is ‘indefensible, unsupported, entirely speculative and basically rather silly’ – and this from a world’s leading scientific supporter of evolution.  Thus, when the cold light of reality shines on this story that it really turns out to be nothing more than a propaganda piece – meant to bamboozle us.  That should make us step back and ask some larger, more fundamental questions.

Biological systems are irreducibly complex

How do irreducibly complex systems evolve slowly and gradually when all the component parts need to be there from the beginning for the system to work at all?  Think now beyond the giraffe neck to the supposed evolution of the fish to amphibian/reptile and then to mammal.  This would have required the two-chambered heart of the fish becoming three in the amphibian and the circulation of the blood change from heart->gills/lungs -> body to a dual cycle of heart-> lungs -> heart -> body.  And then on to four chambered hearts in mammals. How does the heart ‘work’ while it is in-between chambers?  When the circulation system has left the single cycle of the fish but not yet arrived at the double cycle – how does the transitional organism (never found in the fossil record mind you) even survive?  Think about how when we want to ‘just’ adjust valves on our hearts we get the best-trained surgeons, shut the heart down and thus bypass the heart.  With the best of our intelligence we can’t modify the machine ‘while it is running’.  If we can’t make minor adjustments to valves without shutting the machine down and bypassing it how would random chance do any better in changing complete circulation paths and developing heart chambers?  How does something live in the ‘middle’?

Darwin’s Challenge to Darwinism

These examples highlight a fatal problem with the Darwinian story.  Darwin himself stated the seriousness of it:

“If it could be demonstrated that any complex organism existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down”
C. Darwin Origin of Species 6th ed. 1988 p. 154

Yet instead of honestly and directly addressing these challenges textbooks take the approach of developing scenarios in story form.  As my university invertebrate textbook describes the process:

Almost any kind of scenario can be concocted to explain how one group of organisms might have arisen from another.  … narratives are often based on a priori assumptions about hypothetical ancestors. … virtually any complicated evolutionary transition can be described on paper, given enough imagination …
Richard C. Brusca & Gary J. Brusca. Invertebrates   1990. p880

…any number of evolutionary pathways can be .. made to appear convincing on paper by imagining .. hypothetical ancestors or intermediates, but one must always ask whether these hypothetical creatures would have worked?” (ibid. p. 120)

That makes good scientific sense!  Let us ask whether these hypothetical creatures ‘would have worked’!  When we do that, when we observe how interconnected systems need all the components in order to function at all, when we recognize that for all machines and systems (like my website) non-trivial modifications require that the machine be shut off until are the components properly integrated then we can see the difficulty of the Darwinian claim.

But it seems like the whole educational and academic enterprise rather prefers to push misleading ‘stories’ in the name of science.  When one sees how stories are ‘concocted’ with ‘imagination’ to ‘bamboozle’ us we may want to ask – Does the emperor really have any clothes?

Maybe it is worth a more thorough investigation.  Perhaps a good place to start is a university debate I participated in (link here), and a critique of human evolution I did in a university anthropology class (link here)

The Faith of a World’s leading Evolutionary Anthropologist

Recently, evolutionary anthropologist Richard Leakey, famous for being the son of Louis and Mary Leakey, and for discovering the Turkana boy hominin fossil, had gave a revealing interview. Here is an excerpt.
“In an interview with the Associated Press (AP), Richard Leakey, a 67-year-old, Kenyan-born Stony Brook University professor, paleoanthropologist, and avowed atheist, said that he believed scientific discoveries over the next 15 to 30 years will have reached the point that “even the skeptics” will be able to accept the theory put forth by Charles Darwin in his 1859 book Origin of Species.”

The Faith of Richard Leakey

Leakey here touches on a point that I find curious. He ‘believes’ future discoveries (and rather far in the future) will prove to be so convincing that people will have to accept non-design explanations. But is he saying this as a scientist? Observation is the cornerstone of the scientific method. But how can we ‘know’ what we will observe in the future? In point of fact, there is no scientific way to know what we will observe in the future. The scientific method is inherently limited to observations that can only be made in the present. So what is the basis by which Leakey makes his predictions for future observations? It is by faith pure and simple.
When Richard Leakey says this, he is not speaking as a scientist, but as a believer. This shows that everybody, secularists and atheists included, has faith in something that cannot be proven by observations made today. Leakey may be right and perhaps observations will be made in the future, but that belief cannot be proved or disproved today – it can only be believed or not believed.

University Evolution Text summarizes most compelling evidence for Evolution

But we can, using reason and logic from observations we have on hand today make judgments. So let’s continue where we started in the last post to look at similarities in architecture across the biological world. The quote below is taken from a university text entitled Evolution and from the chapter entitled ‘Evidence for Evolution’. In going to this source we drill down to the nub of the matter to look at the foundational evidence on-hand today.
Patterns of Relationship provide the Most Powerful Evidence for Evolution
Although direct observation and the fossil record each provides powerful support, the most compelling evidence for evolution comes from the patterns of similarity between present-day organisms, which reveal features that are shared across all organisms: a nested pattern of groups within groups, consistent across many different traits, and a correspondence between biological relationship, geological history, and geographical distribution
Universally Shared Features [subcaption]
The full extent of this similarity [of biological life] was revealed when the universal principles of molecular biology were discovered in the middle of the last century. Almost all organisms use DNA to encode their genetic information, which is transcribed into RNA and then translated by a single universal genetic code into protein sequence. … Indeed the basic machinery of replication, transcription and translation is conserved across all living organisms. The success of molecular biology lies in the essential universality of its mechanism….  Any code that maps the 64 triplet codons onto the 20 amino acids would work and could be implemented just as easily by an appropriate set of tRNAs. Evolution 2007 by N.H. Barton, D. Briggs, J. Eisen, D. Goldstein, N. Patel.  p66-67
In other words, this textbook is saying that if we want to get directly to the most compelling hands-down evidence that we have observed in the last 100 years for evolution it would be that there is the same DNA code across all organisms, that there is a secondary (and also universal) code in the RNA to transfer the information stored in the DNA to the protein assembly, and that this code universally maps ‘triplet codons’ (i.e. 64 sets of three DNA/RNA instructions) to the 20 different amino acids (which are like the ‘letters’ used to build the long protein string out of which we are made).

Bioinformatics Text: Human Designed Information System Architecture

In my previous Post I introduced the textbook on Bioinformatics – the science of mapping and storing genetic information on computers worldwide so that this information can be analyzed by scientists. Here is how this science is described.
As mentioned primary databases are central repositories and distributors of raw sequence and structure information. They support nearly all other types of biological databases … therefore in the biological community there is a frequent need for the 2ndary and specialized databases to connect to the primary databases and to keep uploading sequence information… All these create a demand for linking different databases. The main barrier to linking different biological databases is format incompatibility as current biological databases utilize all three types of database structures. Essential Bioinformatics. 2006.  Jin Xiong. p16-17
In other words, biological information scientists, in order to design a robust and efficient genetic information storage, retrieval and processing system to conduct their research with have: 1) primary databases, 2) secondary databases connected to this primary database to process specific information, and 3) a major problem is that there are different database structures that are not compatible.
Let’s make a comparison between the genetic architecture of information in living organisms and that designed by information scientists by putting these quotes side-by-side
The ‘most compelling evidence for evolution’ quoted in evolutionary text
Information science quoted in Bioinformatics
“…all organisms use DNA to encode their genetic info”…
“…primary databases are central repositories and distributors of raw information…”
“which is transcribed into RNA and then translated by a single universal genetic code into protein sequence.”
“…in the biological community there is a need for the 2ndary databases to connect to the primary databases…”
“…Indeed the basic machinery of replication, transcription and translation is conserved across all living organisms…”
“… All these create a demand for linking different databases.”
“The success of molecular biology lies in the universality of its mechanism….”
“…The main barrier to linking is format incompatibility as current databases utilize 3 types of structures…”
When placed side-by-side, we can see that the architecture of both systems are described very similarly. In both there is a primary database (the DNA in organisms) housing the raw information, secondary databases (RNA in organisms) to transfer this information to processing sites, and finally the processing sites (protein assembly in organisms). The only real difference is that the human engineered system is NOT universal and this creates problems in the implementation of the human designed system. In other words, if the human system had a universal structure, like the information system in nature, it would be better designed and more efficient.
The reason that there are different structures in the human systems is that there were different researchers that began this work in different parts of the world. If they had coordinated their efforts from the beginning they would have adopted one universal system. However, since bioinformatics is an architecture designed by intelligent agents the obvious parallel to the genetic information system in nature is that of being designed by a Mind. The fact that we observe (today!) one universal genetic system that stores, retrieves, utilizes and duplicates information at an efficiency, speed and fidelity that information scientists are still striving to achieve, speaks volumes to the inference that there is One Design Mind behind it all.
In fact, if chance and random processes has produced the one natural information system that we do observe, and this same chance and random processes have been in operation through all time why do we find no evidence in organisms today, or from those of the past, that there has ever been another information system architecture that has also arisen by these same natural processes? If there were several different systems out there we could deduce either that there were several designers out there (like the Greek Gods of old) or that indeed there is a natural process that spontaneously develops information system architectures.
This is why Leakey must appeal to the unobservable future, and base his appeal on faith, pure and simple, because the fact of the matter is that the ‘most compelling evidence’ we do observe today actually infers a Design cause much more naturally than a mindless natural cause. But though it may be more logical and reasonable from the observations we make today, it is far less popular. Therefore world-leading evolutionary scientists, like Leakey, by faith “are sure of what they hope for and certain of what they do not see”
Why should we form beliefs simply from world opinion shapers when theirs is simply faith anyways?  Why not investigate for ourselves?  Here is a good place to start on a biblical theme and here is a good intro on human evolution – Leakey’s specialty.

Computer super-virus shows anomaly of evolutionary thinking

News broke out in global media outlets at the end of May about the most sophisticated computer malware virus ever discovered. Dubbed Flame, it has infected hundreds of computers across the Middle East. Here is how media outlets describe it:

From Macleans

Kaspersky Lab, a Russian cyber security firm, has discovered that thousands of computers in the Middle East (mostly government machines, mostly in Iran) have been infected with a malicious piece of software they are calling Flame. Flame is insidious, destructive, and very cool. And no one will ever take credit for building it.

Similarities between Flame and the Stuxnet and DuQu viruses are leading to speculation that the programs were all created by the same people. Stuxnet, which bloodlessly set back the Iranian nuclear program by as much as a decade, is widely believed to be the product of an Israel-America cyberweaponry team-up. Of course, neither country has confirmed this.

From Discovery News

The most sophisticated and powerful cyberweapon to date — a Swiss Army Knife spy tool that can evolve and change to deal with any situation — has been discovered on the loose in several Middle Eastern countries, security researchers said Tuesday.

The Worm.Win32.Flame threat, or “Flame” for short, was likely built by the same nation-state responsible for the Stuxnet virus that targeted Iran’s nuclear power plant in 2010.

Flame can grow and change, too: What makes this cyberweapon so powerful is the ability to be reconfigured with new modules that turn an infected PC or industrial control system into whatever tool a spy dreams up.

From CBN

Experts see similarities between Flame and the Stuxnet virus, which disrupted Iran’s nuclear centrifuges in 2010. Stuxnet was widely believed to be the work of Israeli intelligence, leading to speculation that Israeli programmers may have struck again.

From Surface Earth

According to a wired.com report, The Flame virus is twenty times more complex than the Stuxnet virus , which struck Iran’ s nuclear facilities in 2007. Flame can take screenshots, and capture messages sent over an infected network, and even use the computer’s microphone to record conversations.

The experts believe that this level of complexity indicates that Flame was created by a government rather than an individual criminal or group of hacktivists. Commentators quoted in the Telegraph have suggested that Israel, China, or the United States may be responsible. Israel and United States were widely suspected of creating the Stuxnet virus, and Iran claims that it has noted significant similarities between Flame and Stuxnet, although the western cyber security firms investigating Flame disagree.

From National Post

He said there was evidence to suggest the code was commissioned by the same nation or nations that were behind Stuxnet and Duqu, which were built on a common platform.

Both Flame and Stuxnet appear to infect machines by exploiting the same flaw in the Windows operating system and employ a similar way of spreading.

That means the teams that built Stuxnet and Duqu might have had access to the same technology as the team that built Flame, he said.

From New York Times

Flame, these researchers say, shares several notable features with two other major programs that targeted Iran in recent years. The first virus, Duqu, was a reconnaissance tool that researchers say was used to copy blueprints of Iran’s nuclear program. The second, Stuxnet, was designed to attack industrial control systems and specifically calibrated to spin Iranian centrifuges out of control.

Because Stuxnet and Duqu were written on the same platform and share many of the same fingerprints in their source code, researchers believe both were developed by the same group of programmers.

From The Globe and Mail

In addition to its massive size and many modules, the software’s sophistication is evident from the way it infected machines in the first place. To get on a host computer, Flame was designed to provide a fake Microsoft security certificate. Pulling that off, experts say, would have required incredibly advanced knowledge of cryptography, indicating that math geniuses were among Flame’s authors.

Notice what these articles tell us that software security experts are deducing:

  1. A common design team developed both the Flame malvirus and the earlier discovered Stuxnet and Duqu viruses because of similarity in architecture between them.
  2. The ability of Flame to adjust and change (evolve) means that experts and resources on the level of nation states are behind this virus. This was not made by a bedroom hacker.
  3. Complexity of the malware is broadly measured by its functionality. It can do many things, more things than Stuxnet, and is thus considered more complex.

This reasoning and these deductions seem so reasonable to us that we, without much thought, follow along in their line of reasoning. And that should make us re-think another line of reasoning that is directly confronted by this logic. Notice what the following university textbooks quotes tell us about evidence for naturalistic evolution.

It became apparent that animal species that were similar in their anatomy also had similar genetic instructions. Researchers have also shown that, even though the wing of an insect and the arm of a primate look very different, the same basic instructions are used during their development. … The only explanation for these similarities and this connectedness that has withstood scientific scrutiny is evolution, and the only mechanism for evolution that has withstood scientific scrutiny is natural selectionBernard Wood. Human Evolution. 2005. p. 22

Hox gene expression provides the basis for anterior-posterior axis specification throughout the animals. This means that the enormous variation of morphological form among animals is underlain by a common set of instructions. Indeed hox genes provide one of the most remarkable pieces of evidence for deep evolutionary homologies among all the animals of the world.  Developmental Biology 8th Ed. 2006. SF Gilbert. p. 725

These two university textbooks (and many others could be cited) are telling us that similarity in genetic code is ‘one of the most remarkable pieces of evidence for deep evolutionary homologies’.   Really?  So why does similarity in code between computer viruses indicate to computer experts a common design team behind them?  These are very analogous comparisons and yet the conclusions drawn are opposite.

So how strong is this evidence for evolution? A couple of years ago, because of my background in software development and database design I picked up a university textbook dealing directly with sequencing of genetic information and storing that information in computer databases. Note how an expert in DNA sequencing data sees similarity in genetic information.

It is important to distinguish sequence homology from the related term sequence similarity because the two terms are often confused by some researchers who use them interchangeably in scientific literature. To be clear, sequence homology is an inference or conclusion about a common ancestral relationship drawn from sequence similarity comparison when the two sequences share a high enough degree of similarity. On the other hand, similarity is a direct result of observation from the sequence alignment. Sequence similarities can be quantified using percentages… In dealing with real research problems the issue of at what similarity level can one infer homologous relationships is not always clear … Essential Bioinformatics Jin Xiong 2006 p 32

In other words, the homology (i.e. evolution) is just an inference from the data. Therefore other inferences could also explain the data. But Xiong notes that the scientific literature ‘often’ (his word) confuses the inference with the data itself. If this is the case, then these researchers will not recognize other inferences since they think that their inference is really data.   The issue is not with the data, but with the mind interpreting the data.

The inferences drawn from the experts who reported Flame should lead us all to recognize that there is another good inference that can be drawn from similarity in DNA sequences between organisms. Similarity in code naturally infers common designer. And this makes sense. The reason that the iphone, ipad and the ipod share common features has nothing to do with evolution. They share common features because they share a common design team – those working in Apple. The fact that so many textbooks do not even acknowledge this very natural inference should raise our curiosity. The design inferences from Flame, in a context outside of biology, should prompt us to also consider design inferences in the natural sciences.

We recognize a mind behind the Flame virus because the code shows plan and purpose.  No one disputes this.  We can use this same reasoning to see if biblical events also exhibit verifiable plan and purpose.  You can be the judge, but the remarkable coordination of events separated by thousands of years in the sacrifice of Abraham and the inauguration of Passover lead me to think there is a Mind behind the coordination of these events.  And since they are converging on the same point it is reasonable to deduce that it is the same Mind behind these events, in the same manner that software experts deduce the same design team behind Stuxnet and Flame because of similarities between the two.  This mind is different than a human mind since it also makes verifiable predictions deep into the future.

Interesting to me, these  leading computer software experts were curious about the virus and investigated it with an open mind.  Why should we be afraid to do likewise with this Mind?  We might discover something life-changing.

 

 

1. The Case for God – Considering Design

It is generally assumed in our world today that naturalistic evolution can explain how life arose and developed into what it is today.  In other words, the origin and development of everything from lobsters, giraffes and humans – and everything in between – can supposedly be explained by evolution.

When I was asking some basic questions of the gospel (as summarized in About Me: The Wisdom I learned from a filthy-rich, hard-drinking playboy) I had read books that called evolution into question and argued for a Creator.  However, it was when I was a grad student in Forest Engineering that I decided to study university textbooks and journals used to teach evolution to dig deeper into the subject.  It was eye-opening.  What the critics of evolution wrote was one thing, but it was the arguments and rationales used in the textbooks and journals explaining evolution that moved me far more.  Since my grad student days I periodically read the current textbooks used in university.  In the following four videos I take you on a tour of some of these textbooks so you retrace the journey that I took.

This first video introduces the Design Inference and asks whether such a view, at a high level, fits with the data.  Seeing how leading evolutionists describe what and how life is shows us that there is at least an initial fit.

This second video looks at whether we observe the process of evolution occurring today.  After all, science is based on what we observe.  What do the texts says?…

This third video surveys the fossil record of natural descent and then using the alleged evolution of the bird-lung looks at some theoretical problems with functional transitions.

This fourth video looks at misconceptions that are common in our culture about evolution and then concludes by revisiting Design.

These video sessions reference some of the books and journals that I have studied over the years.  The main ones used in the videos are:

Kenneth V Kardong,  An Introduction to Biological Evolution. 2005

Snustad and Simmons.  Principles of Genetics 2nd Ed 1997

Francis Collins.  The Language of God. 2006

SF Gilbert. Developmental Biology 8th Ed 2006.

Scott Freeman and JC Herron. Evolutionary Analysis 4th Ed. 2007

ENK Clarkson &  Blackwell.  Invertebrate Palaeontology and Evolution. 1979

Peter Price. Biological Evolution, 1996

Davis & Kenyon.  Of Pandas and People: The central question of biological origins. 1993

Blog Posts Related to this Session

  • October 8, 2013 - University survey affirms we are ‘Bound to Believe’

  • June 1, 2013 - Does Evolution make sense in light of biology?

  • September 4, 2012 - …But Corrupted (Part 1 – like orcs of Middle-earth)

  • August 27, 2012 - In the Image of God

  • July 26, 2012 - System upgrades shows hopelessness of Darwinian evolution

  • July 19, 2012 - ConsidertheGospel System upgrade shows hopelessness of Darwinian evolution (Part 1)

  • June 18, 2012 - The Faith of a World’s leading Evolutionary Anthropologist

  • June 11, 2012 - Computer super-virus shows anomaly of evolutionary thinking

  • April 22, 2012 - BBC Reports Startling Genetic Tests – Neanderthal in Your Bloodline

  • April 14, 2012 - What about Human Evolution?

  • February 13, 2012 - From Soapberry Bugs to SuperBugs: Nature’s slippery slide down.

  • February 6, 2012 - Origins: Evolution or Design – why touch it?

  • January 31, 2012 - Antony Flew Considered Intelligent Design

  • January 24, 2012 - The Ubiquity of the Design Inference