Evolution

I’m trying to work out exactly what problem your blog post has with Cytochrome C. It’s not exactly clear.

Perhaps that it doesn’t show an evolutionary pathway from bacteria to man? That’s not what it’s intended to show, nor anything that is practical to show from a single gene. Asserting that evolution must show x without providing any reasons, is not a particularly good argument.

Maybe that it thinks there should have been more change? Firstly: it doesn’t actually matter, as the proof of Cytochrome c is based upon relative differences between organisms. Secondly your blog post seems to indicate that there is no functional constraint for Cyt C not changing - there is. If it changes in a way that alters the function of the protein - the animal dies while it’s still a single cell - so it’s noy going to be inherited.

Other than that, this blog post, and your reply seems more about telling everyone who wrong Evolution is, but providing no actual logical reasons as to why.

It was written by a micro- biologist. I'm sure he will be grateful for your insight into his expertise.

its a non peer reviewed blog posts. I can post you a peer reviewed article by microbiologists that show the details of why Cytochrome C is excellent evidence. As you expect me to believe your blog posts on its own authority - that would be enough to convince you, right?

Now: I explained the detail of why the patterns in Cytochrome c are highly specific and match inferred relatedness. Your blog post doesn’t bother to challenge that at all. If your blog post doesn’t challenge the pattern, nor why the pattern was relevant, there’s not too much to say.

As I pointed out though, this microbiologist makes two fatal and scientific errors. Firstly this microbiologist seems to think that Cytochrome C can undergo lots of changes which as I pointed out (and you ignored), means there is a functional constraint.

Secondly, the microbiologist moves the goal posts by trying to misrepresent what Cytochrome C actually showed - which I already explained - and you seem to ignore.

My post on Cytochrome C actually provides the detail of what it is intended to show, why the pattern is relevant, and why it supports evolution.

This person only seems to have made these two arguments, and simply claiming the evidence is absent as a result is not scientific and illogical. Especially as I have explained in detail what the evidence Is and why it is relevant.

Perhaps you would care to offer more details, rather than simply writing posts emphatically telling everyone how wrong they are, but providing no detailed explanation or justification of why.

Excellent posts. Thank you.

The biggest problem with the next part of the set of evidence, is what it really means, and what the science is trying to show. The conceptual nature of genetics, and the evidence from it that supports evolution is both intuitive and massively compelling - once you understand the conceptual nature - but it’s this understanding that trip up most people; and what most scientists fail to explain properly.


So, what I wanted to do, is start off with a thought experiment - to explain the conceptual nature of what all scientists are talking about when it comes to genetics, evolution and common descent. This is not an exact analogy - nor intended to be: but its intended to illustrate the core concepts:


Let’s say many, many years ago there was a really tough university course for which you had to write a paper.

One day, a super smart guy writes a great paper and his class mates get hold of it. Each decide, instead of writing their own, they will take a digital copy of the paper, make a few changes and submit it as a new paper.

When they make changes they:

• Introduce the odd typo here and there.
  
• Change a few words when they feel it makes sense.
  
• Occasionally they make a mistake and copy a paragraph by accident, or remove a paragraph.
  

The next year, the paper is requested again - the next set of students ask various people they know who took the course before to share their paper from last year - and the students go about copying it again. Some of last years students get copied multiple times - others not at all.

This goes on for year - the classes get larger, and the paper shared and copied by more and more people. Each year, papers are just copied and copied - no one ever writes their own.

Many years later - a university professor analyzes hundreds of thousands of paper this years papers from across the country, to try and work or whether all the work is original - or if it is a copy of some other work: 

If we assume (again remember this is not intended to be an exact analogy), that the papers are all really, really long, and each paper today has been copied hundreds of thousands of times from the original first article:

Can the Professor tell whether they’re all copies of the same original paper? How could he do that?

Could he piece together a rough hierarchy  of papers?

What if found fragments of past paper - how could he use this to confirm or reject the assumed relationship between papers?


All these questions are part of the fields called “Bioinformatics”, which is about the analysis of biological data. As a neat piece of information - BLAST - which is a software tool used to compare genetic relatedness between species has also been used to detect plagiarism in academic papers.

We are distinguishable from our parents and grandparents, and so on.

I think everybody can wrap their head around that aspect of evolution, that life reproduces with variance. 

Firstly, you don’t give me much to work with: it seems your unable to do much more than vitriolic rants about how wrong I am. I’m trying to actually disentangle what those reasons actually are.

The microbiologist explicity states that there should be more change: which isn’t a valid argument against why this is invalid - as it’s really the pattern that’s most important. In addition a microbiologist makes a major error by assuming tha any of the residues aside from 18 can change in any way - which is false.

Despte you shouting at me that I am wrong, what that Microbiologist is factually inaccurate.

Now, Secondly: you claim that the pattern in Cytochrome C does not match more than a couple of species that I mention. That is also factually incorrect. The original tests - and subsequence gene sequencing shows the expected evolutionary pattern across the board. You can even look at the sequences on a free site:

The idea that Cytochrome C should see a progression from lower life form to higher is indicative of your failure to understand what is being tested and how evolution actually works.


If Yeast and anomal share a common ancestor, 800mya, at that point their cytochrome C genes diverge.

If the animal branch them diverge at 400mya into protostomes and deutorostomes their genes diverge again.

And lizards and therapsids 150mya - the genes diverge.


You, and the microbiologist are expecting that lower life forms closer to yeast should be closer in sequence. And show progression.

Erm. No.

Why?

Because yeast didn’t stop evolving the moment the branches diverged. We’re not testing the animal at the time genes diverged, but their descendants alive today.

Both the “animal” branch and the “yeast” branch has been acquiring 800mya of changes to their gene. Everything on the animal branch, and everything on the yeast branch will have about the same number of differences as a result.

Every protostome and every deutorostome will have 400mya of differences when being compared.

Every descendent of lizards and mammals will have 150mya worth of differences between each other.


The CytC pattern is not a measure of how complex, or evolved an organism is - that is a laughable lack of understanding of what CytC is trying to achieve. CytC is a measure of how log ago two species diverged.

Jellyfish and yeast, and humans and yeast all diverged at the same time (multi celled animals), so will show the same numbers of differences when compared to yeast.

However jellyfish and humans will show a little less difference when compared to yeast - but still a lot. As they diverged later - but still a long time ago.

Lizards and humans again - will be around the same number of differences when compared to both jellyfish and yeast - but fewer when compared to each other - but still more than comparing two mammals.

So no, what you and the microbiologist are claiming the pattern should be is absurd, and lacks basic understanding in how evolution works, and what top down genetic analysis is actually intended to show.


As a result - it is readily apparent that the microbiologist - who should know better - is being deliberately dishonest, and deliberately distorting and lying about the science.

It’s more than that: As the error Ethang makes shows.

its at the comparative genetic level - we only have species that are alive to compare: the leaves of the tree. The genetic comparisons are all comparing differences between the leaves to allow them to compare which branch each leaf is on with respect to all the others.

Ethang shows the common faulty thinking that somehow we are seeing archaic DNA or information from the past when peforming the analysis. It’s a big conceptual hurdle and - ironically - the whole reason I used the plagiarism example.

Cytochrome c would be like a recognizable paragraph you see in all of the papers - and comparison of errors between those two sentences is what’s being done. All of the papers have been copied thousands of times, so each of them have many errors compared to the original, but papers that diverge recently have fewer differences compared to ones that diverged in the first or second year. 

>it seems your unable to do much more than vitriolic rants about how wrong I am.

Lol. Vitriolic rants?

>I’m trying to actually disentangle what those reasons actually are.

No you aren't. You're using emotive language to insinuate an image of me. You do this because your case isn't strong.

>Despte you shouting at me that I am wrong....

How am I shouting at you? Did I use caps? If you perceive me "shouting" at you, it could be your conscience. You are wrong, I said so. How was wrong in saying so?

>...you claim that the pattern in Cytochrome C does not match more than a couple of species that I mention. That is also factually incorrect.

It isn't. In your comments to MoPac you contradicted yourself. For example, according to Cytochrome C, the snake is equally distant from an earthworm and a bird.

>The original tests - and subsequence gene sequencing shows the expected evolutionary pattern across the board.

Untrue. You get different patterns depending which gene you use.

>you’re parroting from the biologist…

Again with the innuendo. When I quote a biologist, you say I'm parroting. But if I use my own knowledge, you claim it isn't peer reviewed.

I can and will beat you without the smarmy innuendo. My case doesn't need emotional misdirection.

>Because yeast didn’t stop evolving the moment the branches diverged. We’re not testing the animal at the time genes diverged, but their descendants alive today.

False. Nothing has stopped evolving. All organisms have had an equal amount of evolution. You, in your comments to MoPac, brought up the divergence issue. It was basically incorrect.

>CytC is a measure of how log ago two species diverged.

And you get different times depending on which gene you use. That is why you showed only the results which agree with you.

National Academy of Sciences biologist Lynn Margulis has had harsh words for the field of molecular systematics, which Hillis studies. In her article, “The Phylogenetic Tree Topples,” she explains that “many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”

Unfortunately, one assumption that these evolutionary biologists aren’t willing to consider changing is the assumption that neo-Darwinism and universal common ancestry are correct.

Let’s deal with the outright falsehoods first:

Firstly - you are dishonestly quote mining Lynn Margolis. Who was talking about bacterial and single cellular life - which was assumed to fit a tree until lateral gene transfer was discovered and showed the relationships cannot therefore be described by simple descent. Trying to dishonestly portray her words as applying to the wider tree with regards to eukaryotes, and multi cellular life is massively dishonest.

Secondly - you incorrectly portray me talking about the patterns found in Cytochrome C as if I’m talking about all proteins. That is a intentional misrepresentation of what I’m saying. It’s clear I’m talking exclusively about Cytochrome C, making this a straw man.

Thirdly, you and your blog post asserted that we should see progressive differences in the genes from lower to higher organism. Which would mean that when species diverge: one side of the branch would have to stop changing in order to produce your asserted pattern. As you point out, that’s ridiculous as organisms don’t stop evolving. Unfortunately - as I pointed out in my reply - that’s the error you and you’d cited argument make. As you don’t seem to have provided any defense of this claim other than this rather bizzare deflection, I will presume you don’t have any defense of what you said.

Fourthly you are confusing absolute and relative measurements - Cytochrome C is not an absolute perfect chronologically accurate clock. There are too many unknowns to use this comparative differences. but it is a good relative time indicator. It only has to be accurate enough to show that A is longer than B. The whole point of Cytochrome C is that it demonstrates that relative time - the relative divergence of species - in the same way as other methods of determining orders of diverge.

Finally, as you don’t bother providing a link for your claim that earthworms are closer to lizards than birds - I made the mistake of trying to actually find out your claim - and unfortunate - I can’t seem to find any examples of earthworms in the free gene comparison databases. 

A wider search - and I can find no news, studies or anything else that supports your claim either. The blog post you cited DOES make mention of almost exactly what you said - but uses humans instead of earthworms. So I don’t know if you misquoted or invented it. Either way, I can find no valid source to your claims, so I’m going to call shenanigans. Perhaps you got the comparison wrong, or we’re not comparing the same Cyt C gene - without your source I can’t tell.

What I will do is provide a similar example from free genome databases.

Chickens and anoile lizards diverged a few hundred millions years ago, so are close compared to fruit flies. Armadillos and Hamsters and Chickens and anoil lizards all diverged from the fruit fly at the same time - so chickens and lizards should be fairly close - and all those four animals should all have about the same differences compared to fruit flies as each other.

Which they do:


Bird - lizard
http://useast.ensembl.org/Gallus_gallus/Gene/Compara_Ortholog/Alignment?db=core;g=ENSGALG00000011020;g1=ENSACAG00000013076;hom_id=10580613;r=2:31819123-31821634

Bird - fruit fly
http://useast.ensembl.org/Gallus_gallus/Gene/Compara_Ortholog/Alignment?db=core;g=ENSGALG00000011020;g1=FBgn0086907;hom_id=11355293;r=2:31819123-31821634

Lizard - fruits fly 
http://useast.ensembl.org/Anolis_carolinensis/Gene/Compara_Ortholog/Alignment?db=core;g=ENSACAG00000013076;g1=FBgn0086907;hom_id=11352430;r=6:31328170-31339393;t=ENSACAT00000013078

Armadillo - fruit fly
http://useast.ensembl.org/Drosophila_melanogaster/Gene/Compara_Ortholog/Alignment?db=core;g=FBgn0086907;g1=ENSDNOG00000031540;hom_id=11353514;r=2L:16715891-16719635

Chinese hamster - fruit fly.
http://useast.ensembl.org/Drosophila_melanogaster/Gene/Compara_Ortholog/Alignment?db=core;g=FBgn0086907;g1=ENSCGRG00001022144;hom_id=11356589;r=2L:16715891-16719635


This pattern broadly repeats any way you measure it - in Cytochrome C and other conserved proteins - strawman aside.

The Lie

(Said to MoPac on this page earlier.)

One way of determining this, is trying to find different ways of measuring relatedness of different organisms - if the tree is indicative of descent, then any way of measuring relatedness should match the tree too.

If the tree says humans and chimps are the closest related extant species - yet another way of measuring relatedness is shoes apples and humans are closer than chimps and humans - if valid this would

Falsify evolution.

Evolution predicts a very specific pattern:

The Truth

To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated:The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.3Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”

So, you appear to have conceded - by virtue of the fact you have no response  - that you misrepresented my argument, that you were quote mining Lynn Margolis, that you and your biologist were in incorrect on the points raised, and that you have no data to support your claims about earthworms.


This reply again, is another fairly dishonest quote mine: both deliberately misrepresenting what I said and deliberately misrepresenting what the quote said.

You deliberate misrepresented what I said, by omitting my next line from your quote: “So the first way this was done, was by finding a common protein all eukaryotes share - one that doesn’t change in form of function”



Your second quote as so many others similar that Creationists seemed to enjoy quote mining - are about bacteria and archea - which due to lateral gene transfer do not follow the pattern of descent required to produce a tree. Animals don’t have that such is why above Eukaryotes the tree pattern is what you see. One famous New Scientist article was about this change in understanding, the failure to create a tree for bacteria. There is a minute number of ways genes can jump between animal groups: hybrids and retroviruses, and both have a very limited effect in the tree.


In addition you can’t use any old protein or gene to prove relatedness - because stuff evolves, and genes can be driven by evolution - meaning it can change a lot in one species or another, disappear in other, in a pattern not related to descent. In fact, to demand that all proteins and genes should be useable is to claim that no evolution happens - which is absurd. That you have - a couple of times now - claimed that this is what I have said, is intentionally dishonest.


Obviously, you don’t appear to care what is absurd or not, or what is said or not, but there is a difference between those type of genes and conserved genes - that do not appear to be subject to any significant evolution - but can still undergo random non-functional changes.

Conserved genes do produce the same trees, as do multiple other measures of relatedness from DNA and taxonomy: which is why it’s called a “twin nested Heirarchy”. 

For conserved protein analysis - they will often produce different results: one will say the Norwegian tree shrew is closer to regular tree shrews than African tree shrews, or vice versa: one may put bats closer to rodents than to basal primates, and they may change the inferred order of the 10 or so worm phyla.

You’d obviously expect that, when analyzing proteins that have undergone millions of years of incremental random changes. In the same way you don’t expect to turn up 50 heads and 50 tails if you toss a coin a hundred times.

When you need accuracy, you need to put all these different measures together, because in phylogenetics the precise order of tree shrews matter. 


This is a question of accuracy, not validity: because none of these methods:

• Put fish closer to humans than birds
  
• Put boney fish and cartilaginous fish closer together than boney fish and humans.
  
• Put chimps as humans further away than chimps and fish.
  

Or any other relevant example therein.

The Placenta Problem: How Common Descent Fails

Like politicians and pastors, they overstate their cases, and imply any disagreement is immoral. Don't be fooled.

You’ve raised a dozen or so points so far. You’ve been wrong on every one.

1.) You have dishonestly quote mined at least two examples of scientists in the media.

2.) you have dishonestly misquoted me: by omitting a line that put my statement into context. Using that omission to - twice- claim I was saying something I obviously was not saying.

3.) You and your blog post - made a claim about what should be seen in conserved proteins that relies on evolution stopping on one branch

but not the other. And a claim that completely misunderstands the intent of CytC comparrisons.

4.) You’ve claimed earthworms and lizards and birds do not match Cytochrom C patterns. despite me linking you the ensembl

genome browser, and giving you specific examples of what I’m doing, you haven’t bothered to provide any further details.

5.) Youve made claims about chronology that misrepresent what I’ve said: specifically that I’m claiming about relative times of

divergence - and using this to claim I’m talking about absolute times.

So you have repeatedly misrepresented scientists and me, have quote mined, and stated incorrect science which I have corrected. You now seem to have dropped everything you have claimed thus far, and moved on to the next manufactured controversy.

Given that your intent here seems to be wholly dishonest, given your misrepresentation: I suspect what you’re doing is just throwing link after link after link at me: while I will demonstrate as wrong (as I have), you will forget you even made the argument, and move on to the next. This is called “throwing sh*t at the wall to see what sticks”.

This is a tactic of Creationists in general. Lie, distort, misrepresent, and bombard with bad logic and poor science to force the rational and reasonable scientists to spend pages upon pages to point out and correct faulty logic and errors: only to have the point dropped and move onto the next. 

You’ve clearly demonstrated you do not intend nor seem willing to engage here in any sort of good faith and I have no doubt that if I correct your faulty understanding with these latest arguments as I have done with all of the ones so far, you will simply produce another set of claims based on the same sort of dishonesty and bad science I have pointed out.

This is how creationists derail sensible discussion, and pretend that there is a “controversy” and prevent any intelligent discussion on the subject.

As such, unless your actually willing to acknowledge anything already said: I think you’re just trying to dishonestly derail a legitimate conversation, and I have no intent of engaging with this sort of petulant childishness. I will go back to talking with people who actually seem interested in science and reason.

Modern Creationist theories have been largely sorted to an attempt to refine explanations of evolutionary theory, just sayin....They require they're own additional substantiation to be tested if we are to contend they are indeed well founded, and sufficiently reliable to build upon our current understanding of the natural world.  You can't be a creationist, point out that your observations of the evolutionary process refute evolution and expect to be taken seriously.  Even if the creator is not confined to the current human condition they/it has to have done things somehow.  Clearly if the creation itself is understood, the magical aspect is just a matter of perspective ignorance.  There is zero evidence that tuna fish were assembled from mud and water or came flying out of the sun.  It appears most likely that before there were tuna, there was some other ancestral fish and we can infer from real time observations that over generations somewhere in the life cycle of living organisms that genetic mutations occur and some being reproduced more than others.  The gist of the theory of evolution and the subset theory of natural section have held up to rigorous testing for over a century although the actual physics are still in the supernatural illusion of ignorance.  Conclusively breaking these theories and starting over again would be a bombshell, a great and coveted achievement from a scientist's perspective.  That's what science is all about.

Over 500 Scientists Proclaim Their Doubts About Darwin’s Theory of Evolution

What about modern evolution?

They're still tweaking it. You know the old story, evolution always changes, but that just means it improves. (wink,wink)

 

Bums, all of them.

Yes: you’ve already dismissed me.

You haven’t, however, said anything that holds up to any scientific or logical scrutiny: nor have you presented any compelling argument that anything I’ve said is wrong or invalid.

But, yes: you’ve dismissed me as I suspect you don’t have the emotional ability to accept the science in question. Which is not a good place to be.

As  I mentioned: you’re simply being unreasonable and largely dishonest.

Also - as of today there are 1400+ scientists whose first name of Steve who have signed a petition supporting evolution: 

Right, you're talking about Darwin. That was over 150 years ago. Of course we've improved the theory since then.

The only direct evidence, ie. observed in laboratory-- of simple-to-comlex or complex-to-simple or lateral evolution is with bacteria. Or at least that is last understood back in the 90's.

Has that changed?

...."But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity."....

I disagree that only directly observed evidence in a laboratory is of note here. But if you want examples of observed speciation, we have plenty. Check out all these suckers as well as all of these.

That is not the “only direct evidence”. 

Even the whole “direct” definition and usage is largely arbitrary - that’s mostly what I covered in my first reply.

My task? Where do you get that notion?

Lets' recap, you offered absolutely nothing but denials and a vague phrase that covers a multitude of failed hypotheses because they couldn't answer certain aspects of evolution. Since you offered nothing, you should receive nothing. 

Forcing others to do your homework simply because you deny the science that you clearly don't understand is dishonest. 

As Ramshutu observed, after someone thoroughly dismantles your argument and exposes your lack of scientific understanding, rather than trying to address any of their points (I suspect you know you can't),  you ignore everything they said and bring up some other Creationist talking point. One can't help but conclude that you have little interest in making a good faith attempt to understand the science behind evolution.

In another thread, you demonstrated that you do not even grasp simple inheritance. You asserted that a mutation in one copy of a one parent's gene has a 1/4 chance of being passed to an offspring, when anyone who has taken high school biology should know it is 1/2. Anyone can look up Cistic Fibrosis for an example.

You evolutionists sure do suspect a lot. And let me guess, your suspicions are the same as reality right?

Shhh! If you say nothing about it, it'll be like it doesn't exist.

If you read the article, you would find that everyone involved supports evolution and have merely found a better way to classify and categorize.

It would be like me saying I have a large basket of blue balls and you would come along claiming that was a false statement, that in fact the basket actually contains Navy Blue, Indigo Blue and Sky Blue colored balls.